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The NRCVAX Crystal Structure System
----------------------------------A.C.Larson, F.L.Lee, Y.Le Page, M.Webster, J.P.Charland & E.J.Gabe
Chemistry Division, NRC, Ottawa, Canada, K1A 0R6.
Table of Contents
Introduction ............................................
System Data files .......................................
System Menus and Help Facilities ........................
System Free-format Terminal Input and Defaults ..........
System Structure and Routines ...........................
CREDUC SYSABS ..........................................
CDFILE ABSORP DATRD2 ..................................
PATVEC SOLVER MLTN80 FOURR
..........................
UNIMOL CDEDIT DISPOW DISANG ..........................
COFOUR PLTMOL PLUTO
ORTEP
..........................
PACKER LSTSQ
MISSYM ERRANL ..........................
TABLES UTILTY ..........................................
BRANDX ..................................................
IDCDRE PPLP
..........................................
System Implementation ...................................
System Parameters .......................................
Test Data ...............................................
VAX System Implementation ...............................
UNIX System Implementation ..............................
System Specific Routines & Non-VAX Implementation .......
System Timing ...........................................
System Reference ........................................
Appendix 1. Explanatory notes for ABSORB ...............
Appendix 2. Explanatory notes for DATRD2 & IDATA .......
Appendix 3. Explanatory notes for MLTN80 with NRCVAX ...
Appendix 4. Explanatory notes for CDEDIT ...............
Appendix 5. Explanatory notes for LSTSQ with Batch ......
Appendix 6. Explanatory notes for LSTSQ with Rigid Groups
Appendix 7. Explanatory notes for ORTEP with NRCVAX ....
2
3
4
5
6
8
9
10
11
12
13
14
15
16
17
19
20
22
23
26
27
27
28
34
38
40
47
48
63
Appendix 8. Explanatory notes for PPLP .................
Appendix 9. Sample Output Listings for Ruby ............
Appendix 10. CD File Contents ...........................
Appendix 11. RE File Contents ...........................
Appendix 12. NRCVAX TUTORIAL ............................
65
68
83
90
91
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Introduction
-----------The routines
of programs to
and refinement
the subsequent
facilities are
contained in this system comprise an integrated set
perform all computations necessary for the solution
of crystal structures from X-ray diffraction data and
presentation of results. Comprehensive graphics
included.
The system is entirely compatible with Fortran 77 and has been written
to run in a truly interactive fashion. Most routines are menu driven,
with simple terminal input, which can usually be defaulted. Because of
the high degree of interactivity, the best way to learn about the system
is to use it. The tutorial at the end of this manual provides a painless
way of doing this.
The system is completely symmetry general, treating symmetry
constraints automatically. The maximum number of atoms can be specified
when the system is built and it can handle an essentially unlimited
number of reflections. The system contains routines for graphics based
on Tektronix, Printronix and Imagewriter equipment using its own plotting
routine. It is also possible to produce HPGL and Postscript files.
No guarantee can be given that there are no errors in the code, though
it has been thoroughly checked and tested with many compilers and
operating systems. In the event that bugs are discovered or
difficulties experienced contact E.J.Gabe at the address above, by
telephone at (613) 993-2527 or via Bitnet at the address gabe@nrchem.
Versions are available for DEC VMS, Microport System V (UNIX), IBM
VM/CMS and MVS/TSO operating systems. A full version is also available
for PC/XT and AT microcomputers under MS-DOS. For more information and
copies of this version contact Dr P.S.White, Chemistry Dept, University
of New Brunswick, Fredericton, N.B., Canada. Work is well advanced on
versions for Sun and Silicon Graphics (IRIS) systems.
Page 3
System Data Files
----------------The use of files within NRCVAX is extremely simple. For any structure
there are essentially only two direct-access binary files which contain
all information about the structure. Direct-access was chosen because of
convenience in manipulation and speed of input/output.
These two files (Fig. 1) are usually referred to as the
Crystal Data file (.CD), and the REflection file (.RE).
Both files are generated and maintained by the system and for most
purposes the user need not really be aware that they exist. Their names
are automatically picked up by the system routines (see NAMES.ZZ in the
CDFILE section below) which inform the user of which files are in use.
It is very easy for the user to change the files being used, but this is
not usually necessary. It is also very difficult to damage these files
from within the system. It might be worth saving a copy of the .CD file
from time to time during a structure solution, but this is more to save
oneself potential trouble than because something catastrophic may occur.
It is always safe, though not good practice, to use the system escape
sequence (Ctrl/Y on the VAX) to exit from a routine in an emergency.
The .CD file contains information about the space group, cell
parameters, symmetry, scattering factors, general parameters and
atoms. The .RE file, as its name implies, contains reflection
specific information.
Both files use 32-bit variables exclusively. Records in the .CD file
are 100 variables long and data is stored as 8 general records, 1 record
for each atom and 1 trailing record in which the atom name set to 0.
Records in the .RE file are 32 variables long and data is stored 1
reflection/record. There is a trailing record with h=k=l=0. If
necessary, information about h,k,l and -h,-k,-l reflections are stored
in the same record.
Intensity data is always processed from an IDATA file, which is also a
direct-access binary file. A full description of this file and how to
create it is given in Appendix 2.
Several routines use scratch files and write line-printer output
files. Lineprinter output files are always labelled PROGRAM_NAME.OUT,
e.g. LSTSQ.OUT, TORSHN.OUT. They can be safely discarded after printing
or examining. Two files which should be kept - at least temporarily are the peak file (PEAK.DA) from the Fourier routine, which may be used
by CDEDIT, UNIMOL or DISANG, and the phase file, SOLFOU.DA from SOLVER,
which will be needed to generate an E-map. These files can of course be
deleted when they have no further use.
Page 4
Peak files are formatted and can be used to input atomic parameters
into the system from other sources. The file contains the atom name, x,
y, z and the peak height in the format (1X,A6,3F9.5,F7.1). The x, y, z
values can be free-form and the peak height can be ommitted. There are
other, more convenient ways, for incorporating 'foreign' data into the
system however.
A detailed description of the contents of the .CD
and .RE files is given in Appendices 1 and 2.
System Menus and Help Facilities
-------------------------------The routines ABSORP, DATRD2, CDEDIT, PLTMOL, PACKER, UTILTY, BRANDX
and IDCDRE have command menus which will be printed if a wrong command
is given or if <CR> is typed. Other routines interrogate the user for a
small amount of terminal input, most of which may be safely defaulted.
Because of the frequency with which they are run the routines FOURR and
LSTSQ behave somewhat differently. FOURR shows its default settings
automatically and they may then be changed, if necessary. LSTSQ does not
automatically show its defaults, because that would become tedious as
the program is run so often. The defaults may be seen and changed on
request however. PLUTO runs with normal Pluto-like commands and also has
extensive help facilities as well as a program description in the file
PLUTO.DOC.
Page 5
System Free-Format Terminal Input and Defaults
---------------------------------------------All numeric terminal input is read through the routine FREEFM which
allows the user to input numeric data in a very free form. All such
input is filtered for non-numeric characters and invalid sequences,
such as multiple decimal points or incorrectly placed minus signs.
Commas or spaces can be used as field delimiters and leading spaces
are ignored, as are plus signs. The routine does not distinguish
between real and integer numbers and therefore a real field does
not necessarily have to have a decimal point. A comma will always
delimit a field but only the first blank after a number will be used
as a delimiter. E-format input is not allowed, but fractional values
are acceptable.
The routine returns the values of up to 20 real and integer values
and zeroes are supplied for all fields not explicitly typed, which
means that default numeric values can be given with no typing needed,
i.e. routines use a 0 returned value in response to a request for
numeric data to indicate that the programmed default must be taken.
Examples of valid input strings are as follows.
1,2.4,,0
,-3
,604,,,,1.54,1/4
0 604 0 0 0 1.54
A blank line <CR>
gives
and
gives
gives
gives
1.0 2.4 0.0 0.0 -3.0 as reals (plus 15*0.0)
1
2
0
0
-3 as integers (plus 15*0)
0 604 0 0 0 1.54 0.25.
the same.
20 zero values.
Invalid strings are
1..,
1.,2-4,
1,2,A,3
Multiple decimal points
Wrongly placed minus sign
Non-numeric character
All alphanumeric terminal input is through the routines ALFNUM or
YESNO. Both routines accept upper or lower-case input, but convert it to
upper-case. If the string 'DONT DO IT' is passed to ALFNUM the
lower-case to upper-case conversion is not done. The routine YESNO
accepts only y,Y,n,N or <CR> and returns Y or N depending on the
indicated default value in the call to the routine.
NRCVAX makes extensive use of defaults as valid answers to questions
posed at the terminal. These are always indicated at the end of the
interrogative message, before the question mark, as a value in
brackets e.g. (Y) or (Menu). This indicates the value or action which
will be taken if the user responds by striking the Carriage Return <CR>
key. It is not always possible to assign a sensible default answer to a
question and in these cases no default is indicated and the user must
make a valid response.
Page 6
System Structure and Routines
----------------------------The interconnections between system routines and files is shown in
Fig. 1. The 25 main routines are well integrated and communicate for the
most part via the .CD and .RE files.
The IDATA file is the binary intensity data file used by the system
for diffractometer reflection input. The actual diffractometer program
used will vary from one installation to another, and routines are
provided (in BRANDX), which will convert most types of diffractometer
output into IDATA form for processing by the data-reduction routine
DATRD2. The structure of the intensity data file (IDATA.DA) is given in
Appendix 2 to help in writing conversion routines for other
diffractometer types. If this must be done it will help to study the
existing conversion routines (see Appendix 2) before starting.
Conversion routines are available for Nonius (standard and NRCCAD),
Nicolet, Rigaku, Stoe and Philips diffractometers, Picker instruments
controlled by Larry Finger's automation package and Galen Lenhert's
control software.
A more general routine (BRANDX REFIN, see Appendix 2) is available for
converting non-standard reflection data into IDATA form. Another routine
(BRANDX IUCIN) will convert standard I.U.Cr. reflection data to IDATA
form.
Figure 1 shows the interaction of the system routines with the main
system files. Routines are outlined as | NAME | and files as ( Name ).
The direction of data flow is shown by the characters < and >.
Page 7
Figure 1.
Overall System Structure
-------| CREDUC |
-------| SYSABS |-<------------(:::)
-------( I )
(:::)-<-------------| CDFILE |
( d )
(
)
-------( a )
(
)
(Face )-<->-| ABSORP |-<---------->-( t )
(
)
-------( a )
( C )-<----------->-| DATRD2 |-<---------->-(:::)
(
)
|
|------------>-(:::)
( r )
-------(
)
(
)------------->-| PATVEC |
(
)
( y )
-------(
)
(
)------------->-| SOLVER |-<------------( R )
( s )
(:::::)-<---| MLTN80 |
(
)
(
)
(Phase)
-------( e )
( t )
(:::::)--->-| FOURR |--->-(:::)
(
)
(
)-<----------->-|
|
(
)
( f )
( a )
-------( P )
(
)
(
)-<----------->-| UNIMOL |-<---( e )
( l )
( l )
-------( a )
(
)
(
)-<----------->-| CDEDIT |-<---( k )
( e )
(
)
-------(
)
(
)
(
)------------->-| DISPOW |-<---(:::)
( c )
(
)
| DISANG |
(
)
( D )
-------( t )
(
)------------->-| COFOUR |-<------------(
)
( a )
-------( i )
(
)-<----------->-| PLTMOL |
(
)
( t )
-------( o )
(
)
| PLUTO |
(
)
( a )------------->-| ORTEP |
( n )
(
)
| PACKER |
(
)
(
)
-------(
)
(
)-<----------->-| LSTSQ |-<---------->-(
)
(
)
-------(
)
( F )------------->-| MISSYM |
( F )
(
)
-------(
)
( i )------------->-| ERRANL |-<------------( i )
(
)
-------(
)
( l )------------->-| TABLES |-<------------( l )
(
)
-------(
)
( e )-<----------->-| UTILTY |-<---------->-( e )
(
)
-------(
)
(
)-<----------->-| BRANDX |-<---------->-(
)
(
)
-------(
)
(:::)-<----------->-| IDCDRE |-<---------->-(:::)
|
-------PPLP |
--------
Page 8
The 25 main routines are listed in the table below, followed by a
short description of each.
Main Routines
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
CREDUC
SYSABS
CDFILE
ABSORP
DATRD2
PATVEC
SOLVER
MLTN80
FOURR
UNIMOL
CDEDIT
DISPOW
DISANG
COFOUR
PLTMOL
PLUTO
ORTEP
PACKER
LSTSQ
MISSYM
ERRANL
TABLES
UTILTY
BRANDX
IDCDRE
PPLP
(CR)
(SY)
(CD)
(AB)
(DA)
(PV)
(SO)
(ML)
(FO)
(UN)
(ED)
(DS)
(DI)
(CO)
(PL)
(PU)
(OR)
(PA)
(LS)
(MI)
(ER)
(TA)
(UT)
(BR)
(ID)
(PP)
Cell reduction
Systematic absence and space group determination
Generate the initial .CD file
Gaussian and Empiric absorption correction
Intensity data reduction
Patterson vector and simulation
Structure solution routine similar to Multan
The 1980 version of MULTAN
Fourier calculation
Unique molecule builder
Edit the .CD file
Distance, angle and powder pattern
Distance and angles only
Best plane Fourier calculation and plotting
Molecular plotting routine
PLUTO plotting package (Interactive version)
ORTEP plotting package (Interactive version)
Packing diagram routine
Structure factors and least squares
Detect missing symmetry in structures
Error analysis routine
Atomic coords and structure factor tables
Set of crystallographic utility routines
Set of conversion routines for other systems
Set of internal binary/ASCII conversion routines
Powder pattern indexing
(XX) refers to the routine subdirectory name.
1. CREDUC
This routine performs a cell reduction on cell data which may be typed
or from a file. The algorithm is based on the detection of possible
2-fold axes in directions with low indices (J. Appl. Cryst., 1982, 15,
255.). It has successfully processed hundreds of examples - including
all standard tests - and is believed to be error free.
We highly recommend that users run this routine on new cell data
before processing a structure and preferably before collecting any
intensity data.
2. SYSABS
This routine examines an IDATA file for all types of systematic
absences. Statistics are kept and a summary is printed, with possible
systematic absences indicated. Full details of particular reflection
classes with Inet, sigma(Inet) and the ratio of the two may then be
printed for verification. Finally the routine attempts to determine the
space-group from the results. The answers should be treated with
CAUTION. The routine is still experimental and we have not been able to
test it for all space-groups, because of the difficulty of obtaining the
necessary IDATA files.
Page 9
3. CDFILE
This is the routine that produces the initial version of the crystal
data file (.CD) for a structure. It interprets the space group symbol
and generates symmetry information from it. Unit cell and scattering
factor data are also processed and written to the 8 file-header blocks.
The space group code is an upgraded version of the SPGP code from
Allen Larson's LASL system, which processes the short form of the
International symbol, with each discrete operator separated by a blank,
e.g. P 21 21 21 for P212121. (Int. Tab. Vol. 1, p. 44),
P 63/m c m for P63/mcm (Int. Tab. Vol. 1, p. 302),
I a 3 d
for Ia3d
(Int. Tab. Vol. 1, p. 345).
CDFILE also works out the assymetric unit for all types of Fourier
maps, using the symmetry matrices produced by the space-group code.
The routine also produces a file called NAMES.ZZ, which contains the
names of the .CD and .RE files for the structure under investigation.
The name of the .CD file is given as part of the terminal input to
CDFILE, e.g. STRUC, in which case STRUC.CD and STRUC.RE are written to
NAMES.ZZ. The .CD and .RE files are used by most routines and the
NAMES.ZZ file provides a means of access to both of them, without having
to continually retype the names.
4. ABSORP
This routine calculates absorption corrections using a Gaussian
integration or an empirical psi-scan method.
For the Gaussian method the input file is a file with data describing
the crystal faces and an IDATA file from the Picker or Nonius
diffractometers. A full description of the input is given in Appendix 1.
It is possible to plot the crystal shape, in stereo, for checking and
then edit the input if wanted. (See System Implementation for details of
system graphics) Trial calculations can be performed before starting
the main run.
The calculation can be quite lengthy and there is a
command-file given in Appendix 1 for running ABSORP as a BATCH job.
For the empirical route a file of psi-scan data is needed from which a
correction curve is calculated and then used to derive corrections.
Results from both methods are written to the IDATA file and applied by
DATRD2. There is a more complete description of the input to ABSORP in
Appendix 1, together with some examples. These should help users with
the input requirements and also how to adapt the input to local
diffractometer conditions.
5. DATRD2
The data reduction routine accepts intensity data in IDATA form and
processes this data to produce a reflection file (.RE). The input data
can be from the NRC diffractometer routine in standard Picker FACS-1 or
profile analysis form. Data from many other sources can be converted to
IDATA form by routines in BRANDX (see below) These sources can be Nonius
CAD-4 or NRCCAD data, Larry Finger's or Galen Lenhert's Picker control
system, Philips or Nicolet diffractometers, data in standard I.U.Cr form
or data from other sources which can be specified in a general flexible
manner.
Page 10
The routine can process and average multiple data sets and
will automatically distinguish between F(hkl) and F(-h-k-l) where
necessary. Reflections may be scaled in several ways and weights are
calculated from counting statistics or internal consistency for multiple
data sets. Checks are made from symmetry, to ensure that a complete data
set has been collected. Values of Fobs, least-squares weight and up to
12 scattering factors are written to the .RE file. Internal agreement
factors are calculated between symmetry related measurements and
statistics are accumulated for the K(s) curve, from which E and epsilon
values are derived and written to the .RE file.
A more complete description of DATRD2 is given in Appendix 2.
6. PATVEC
Calculate the Patterson vectors in symbolic form for any space group,
and the actual vectors in numeric form for an input positions x,y,z.
7. SOLVER
This is a highly modified form of an early version of the well-known
routine Multan. It accepts input from the .CD and .RE files and can
accomodate up to 1000 E-values with up to 100 sigma2 relationships
per reflection for up to 1024 phase sets. Reflections in the starting
set are automatically selected, but the user can include extra
reflections in order to develop more phase sets. Psi0 reflections may be
used and phases from a partial structure. The routine operates entirely
in-core and as a result is quite fast. It has proved to be very
successful.
The phase sets are written to a file (usually SOLFOU.DA) for input to the
Fourier routine.
8. MLTN80
NORM80 and MLTN80 are available with all the features of that
later version of MULTAN. Only the first 2 routines of the full Multan
package have been implemented i.e. EXFFT and SEARCH, are not included.
The routines M8XIN and M8XOUT are provided in BRANDX to allow NORM80
and MLTN80 to be used easily with the remaining NRCVAX routines. A
command procedure M80RUN.COM is provided to run the complete MLTN80
sequence automatically. (See Appendix 3 for more details.) If this
routine is used, the normal reference should be made to it in any
publication.
9. FOURR
FOURR calculates all types of Fourier maps. It has many options
which may be selected from the terminal. These include origin removal
and sharpening for Patterson maps; Sim weighting for Fourier maps;
correction for anomalous dispersion effects; a variety of print
suppression and format control options if the map is to be printed;
a peak picking section with 27-point fitting which eliminates
symmetry-repeated peaks and writes a PEAK file, and a contouring
facility. Almost all data manipulation is performed in memory and the
routine is quite fast.
Page 11
10. UNIMOL
UNIMOL takes positional data from a .CD file and/or a PEAK file
and makes a reasonable attempt to make a connected unique molecule.
Interatomic distances are calculated, printed and stored in the .CD file
for subsequent use by PLTMOL. UNIMOL provides a convenient way of
picking up a large number of atomic positions in a PEAK file and
inserting them into the .CD file at the beginning of a structure.
Positions so selected will be called PEAKxx and if positions are taken
from several PEAK files it is possible that several of them will have
the same name. It is advisable to use the Peak name change facility in
CDEDIT to avoid this difficulty.
11. CDEDIT
As its name implies this routine allows the user to edit the direct
access .CD file. It is highly interactive and menu-driven. Atomic
information can be entered manually on an individual atom basis or, more
conveniently, read from a PEAK file or a general text file. Symmetry
constraints are generated for input atoms and stored in the .CD file and
the routine automatically fixes appropriate parameters in polar space
groups. Hydrogen atom positions can be generated for a variety of
geometries as long as UNIMOL has been run previously. The .GRP file for
rigid group refinement is also set up by CDEDIT.
Appendix 4 contains an extensive description of CDEDIT.
12. DISPOW (DISANG)
This routine is an amalgam of a distance and angle routine and a
comprehensive powder pattern calculator. Distances can be computed
with or without angles and e.s.ds. Distance and angle limits may
be set on individual atoms though this is not normally necessary.
Powder patterns may be calculated with d-spacings and intensities
in several different standard forms. Input can be from a CD file,or
typed or from a Metal Data File (see the subroutine DSMDRD.FOR).
DISANG is a simplified version of DISPOW which only calculates
distances and angles from a .CD file and/or a peak file PEAK.DA.
If disk space is at a premium this routine should be used because
it is much shorter than DISPOW. There are two output modes for
DISANG. The normal (N) mode produces standard bond/angle output,
and the publication (P) mode produces tabular output in a form
suitable for publication in Acta Cryst. and other journals.
In both these routines and in UNIMOL distances are selected on the
basis of whether the calculated value is less than the sum of the
covalent radii of the two atoms times a multiplier. This multiplier is
normally 1.0 but can be changed during input. Different values are
allowed for distances and angles.
Page 12
13. COFOUR
This routine calculates and plots best-plane Fourier maps for arbitrary
plane orientation. Planes may be defined in several ways using atom
names,
atom numbers or general x,y,z positions. Unsmoothed contours may be
drawn
quickly on the screen prior to plotting smoothed contours on any of the
hard-copy devices available.
14. PLTMOL
This routine uses data from a .CD file to draw stereo pictures of
inorganic or organic structures on any of the graphics devices available
to the system. The routine is extremely fast and has proved to be
very useful in the solution of structures and in the interactive
preparation of drawings for publication. Atoms in the file may be
deleted from the screen and a new .CD file written. UNIMOL must be used
in order to make a unique molecule the first time PLTMOL is used. Once
the molecule is assembled however PLTMOL can generate its own
connections.
* Users are strongly urged to try to use this routine either with
Tektronix hardware or one of the many compatible devices now available.
It is wise to configure the system with the three commands identified
in NRCLOGIN.COM for the plotting routines to run successfully.*
15. PLUTO
This is a version of the well-known plotting routine PLUTO, which
has been adapted for use with NRCVAX. It is set up to run with any
of the plotting devices and all plot calls are isolated to routines
which are listed at the head of the main routine. This version of PLUTO
is highly interactive and there are extensive 'HELP' files.
16. ORTEP
This is an implementation of the well known routine ORTEP-II. It reads
all atom and symmetry information from a .CD file and accepts normal
ORTEP and symbolic commands in an interactive way to generate drawings.
Several commands have been added to facilitate this interaction. 1104(RF)
accepts and saves a series of ORTEP commands from a named file, and
1200(ST) turns on the stereo facility for plotting complete stereo
drawings. The stereo option can be disabled with a second ST command.
Once an instruction sequence has been saved, the commands MA and ZM
magnify and zoom the picture, RO rotates the picture and DM redraws it.
It is the users responsibility to supply a file of normal ORTEP commands
to generate the picture. The terminal is the default plotting device.
The command 201(P4) sends the picture to the plotter and automatically
generates the command 203 to re-enable the terminal. The command PT
generates a file for plotting on any of the hard-copy devices available.
Some of the more sophisticated labelling with perspective and print
rotation have not been implemented. If this routine is used to produce
drawings, reference should be made to it in any publication.
See Appendix 7 for a more complete description and examples.
Page 13
17. PACKER
This routine prepares packing diagrams for any of the standard
plotting devices. The routine can deal with all types of molecular
symmetry for up to 12 molecular fragments in a structure. It is very
easy to draw complex diagrams to illustrate packing details and H-bond
schemes. Unit cell box limits can be set and molecules are included in
the plot if the molecular centroid falls within the limits of the
specified unit cell box. A second type of plot allows molecular
fragments which fall within a packing shell to be plotted aruond a
central molecule. Pictures can be further editted by the deletion of
specific molecules and specific bonds may be inserted to emphasize
particular points.
18. LSTSQ
This is the general structure factor and least squares calculation
routine. The system in general and LSTSQ in particular can handle up to
NATSIZ atoms. As supplied, NATSIZ is set to 300. LSTSQ will allow
refinement of up to 2*NATSIZ parameters by the full matrix method or
9*NATSIZ parameters in the block diagonal mode. In the blocked mode,
atoms are not linked and up to 10 parameters/atom may be refined occupancy, x,y,z and 6 uijs. The chirality parameter, eta (Rogers D.
Acta Cryst., 734, A37, 1981), can be refined for non-centrosymmetric
structures, but this should not be done until the end of conventional
refinement. See Appendix 4 for details.
The precise path of the calculation, refinement on Fo or Fo**2, number
of refinement cycles and type of output can be controlled from the
initial dialogue. The progress of refinement can be checked by a
judicious use of the printout control parameters for 'bad' reflections.
Many sequences of refinement cycles may be undertaken in the same
program run. For larger refinements, with the full matrix method, the
cpu time and elapsed time required may become very lengthy and a file is
shown in Appendix 5 to allow the routine to be run as a batch job.
Appendix 6 contains details on the use of constraints with LSTSQ. There
is also a version of LSTSQ for the Analogic AP500 Array Processor, which
is approximately 10 times faster than the VAX 11/780 FPA version.
During a run the current reflection and agreement indices are reported
every 20 reflections at the top of the screen. The first 20 reflections
are always printed on the first cycle of any run, for checking purposes.
19. MISSYM
This routine can detect possible missing symmetry in structural data
which may have been described in the wrong space group. Unit cell and
atomic parameters are taken from a .CD file and an exhaustive search for
potential symmetry elements is conducted on the full unit cell of atoms.
It is well worth running this routine on a structure in which problems
of this type are suspected or even as a general rule.
20. ERRANL
This routine calculates weighting and agreement analyses as functions
of Fo, Fo**2, sin theta/lambda, h,k & l. It should be possible to use
this analysis, in conjunction with the kFo**2 weighting scheme option
in LSTSQ, to obtain a uniform distribution of residuals.
Page 14
21. TABLES
Tables of parameter values and structure factor listings for
publication are prepared by this routine. Two types of parameter
table are allowed, a) where the routine suggests the number of decimal
places to use, which the user may wish to modify, and b) where the
routine prints the table according to the esds in the .CD file in order
to preserve reasonable significance - this is the preferred option.
22. UTILTY
This is a collection of smaller routines for crystallographic
calculations. It is our current practice to add useful small routines
to this package in order that they may become generally available. The
original large UTILTY has been broken into several logical subprograms
(UTILTY, BRANDX and IDCDRE) in this release of NRCVAX.
A REPORT
B BIVOET
C TORSHN
D BESPLN
E EQUIVS
F ORTHOG
G EQXYZ
H EQHKL
I MINUS
J TRANSF
K NEWCEL
L P1GEN
M SCATFS
N NUNAME
O ESDS
Write a report of the structure determination details from
data written to the CD file by ABSORP, LSTSQ and FOURR.
Select reflns with the most significant Bijvoet differences.
Calculate all torsion angles for the atoms in a .CD file.
Calculate least squares best planes through sets
of atoms by Ito's method. Sigmas are calculated.
Compute short contacts between specified atoms or types
of atoms and optionally move groups of atoms with the
equivalent position transformations detected.
Derive orthogonal coordinates from the fractional
coordinates on a .CD file.
Generate equivalent positions for a set of x,y,z values from
the terminal or a .CD file. Symmetry is obtained from the
.CD file.
Generate equivalent reflections for a given h,k,l input.
Symmetry is obtained from a Laue group number or .CD file.
Convert x,y,z on the CD file to -x,-y,-z.
Transform the coordinates on a CD file and the h,k,l values
in an RE file with a reflection index transformation matrix.
New CD and RE files may be written.
Transform cell data and atomic coordinates according to a
direct-cell transformation matrix.
Generate P 1 .CD and/or .RE files from existing .CD and .RE
files of higher symmetry.
Make up composite scattering factors from 2 normal
scattering factors, and insert the values into a
specified place in a .RE file.
Rename atoms in a .CD file. This is a much more convenient
way of renaming many atoms than the method in CDEDIT.
Insert esds into a CD file from published data.
Page 15
23. BRANDX
This is a collection of routines for converting data to and from
NRCVAX form for several diffractometers and other program systems.
A NONIUS
B FINGER
C NICLAY
D PHILPS
E LENHRT
F RIGAKU
G M8XIN
Convert a Nonius CAD-4 intensity data file to an IDATA
file for processing by DATRD2.
Convert an intensity data file from Larry Finger's system
to Idata form for processing by DATRD2.
Convert an intensity data file from a Nicolet diffractometer
to IDATA form for processing by DATRD2.
Convert an intensity data file from a Philips diffractometer
to IDATA form for processing by DATRD2.
Convert an intensity data file from Galen Lenhert's system
to IDATA form for processing by DATRD2.
Convert an intensity data file from a Rigaku diffractometer
to IDATA form for processing by DTARD2.
Write the input files, MULTAN.CDR and MULTAN.RFL for
MULTAN80 OR MULTAN84, from the information on .CD & .RE
files.
H M8XOUT
I CRYIN
J CRYOUT
K SHXIN
L SHXOUT
M REFIN
N REFOUT
O IUCIN
MULTAN.CDR may need to be edited to establish the complete
running parameters before running either version of MULTAN.
The routine MULTAN84 is not supplied with this package and
should be obtained direct from the Univ. of York, U.K.
Convert the binary phase file from MLTN80 into a form
compatible with FOURR. The file written by this routine is
usually called SOLFOU.DA.
This is the complement to CRYOUT. \LIST 5 output from
CRYSTALS (atomic parameters etc) are converted back to
CDFILE form. It is anticipated that .RE files will already
exist
Use data from .CD and .RE files to create the control file
input to the CRYSTALS structure package. This package has an
extremely powerful least-squares routine in which all forms
of geometric and physical restaint and constraint can be
included. CRYSTALS is not distibuted with NRCVAX but must be
obtained from :-Dr D.J.Watkin
Chemical Crystallography Laboratory
University of Oxford
9 Parks Road
Oxford
OX1 3PD
U.K.
Insert SHELX Atom Parameter File data into a .CD file.
Write a SHELX Atom Parameter File from .CD file information.
Convert non-standard intensity data to IDATA file form for
processing by DATRD2. (See Appendix 2)
Output reflection data (h,k,l,Fo,Sigma(Fo)) to a file, in
a variety of forms and formats, for use with other systems.
Converts standard I.U.Cr. data to .CD and IDATA form. Only
atomic parameter data is converted from the I.U.Cr. file,
because it is so easy to create a basic .CD file with
CDFILE. Reflection data is converted to IDATA form and
P IUCOUT
further processed by DATRD2 to produce the .RE file.
Converts .CD and .RE file data to standard I.U.Cr. form as
described in SCFS-87.
Page 16
24. IDCDRE
This is a set of routines for examining and manipulating internal
NRCVAX binary files.
A
B
C
D
E
CDLIST
RELIST
CDMOD
REMOD
EFLMOD
F FLCOPY
G CDREFM
H CDREBN
I DIFFM
J
K
L
M
DIFBN
LITLFM
LITLBN
SHORTN
N GPADDR
List the contents of a .CD file labelling each item.
List specified reflections in an .RE file.
Modify the contents of a .CD file. (Refer to Appendix 10.)
Modify the contents of an .RE file. (Refer to Appendix 11.)
Examine and/or modify specified variables in any direct
access file.
Copy specified blocks of one direct access file to another.
This is convenient for constructing .CD files from
fragments of 2 or 3 other .CD files.
Convert .CD and/or .RE direct access files to ASCII format,
to facilitate transfer between computers.
Convert ASCII .CD and/or .RE files back to direct access
files.
Convert an IDATA file to ASCII format for transmission
between computers.
Convert an ASCII IDATA file back to direct access form.
Convert a .RE file to a compressed ASCII form for storage.
Convert a compressed ASCII .RE file back to binary.
Shorten an .RE file to save processing time. There are
several options for deletion of reflections.
Add new rigid groups to the GROUPS.DAT file.
25. PPLP
PPLP is a powder pattern lattice parameter refinement routine, which
allows the user to interact with the indexing process to derive improved
lattice parameters from a starting set. Input can be typed, from a file
of film measurements or from a file of Qobs or Dobs values. (See
Appendix 8.)
Page 17
System Implementation
--------------------The underlying structure of the system is quite simple and has shown
itself to be easily adaptable to any computer.
The sources of the 25 main routines are kept in 25 seperate
sub-directories, which are referred to by two unambiguous letters from
the routine name (e.g. LS, ED, PU etc). The source code in these
sub-directories is common to ALL versions of the system. These
sub-directories also contain the command files for compiling, linking
and generally manipulating the particular routine.
There are 2 other sub-directories which are used for other purposes.
The GEN sub-directory contains source and object code which is common
to more than one of the system routines, plus its own associated command
files and again the code is common to all versions. This code could
have been put in a general library, but this introduces complexity and
there is no real advantage to doing so.
The SPC sub-directory contains 'machine sensitive' code which varies
from one version to another. There are 10 files in this sub-directory,
9 of which are routines which isolate the system from differences
between Fortran implemenatations and it is these routines which may need
changing in adapting the system to other computers. The code is heavily
commented and the should be studied before attempting any adaptation.
The 9 routines are :--SETIOU - which assigns logical unit numbers to I/O units and the
length, in bytes, of variables in direct-access files.
IBMFIL - which performs all file OPEN and CLOSE operations.
EDRAW - which performs all graphics and
SEND
which is a subroutine of EDRAW.
LENFIL - which finds the length of direct-access files.
NIDATE - which gets the date from the operating system DATE routine.
NIOR
- which isolate all calls to the operating system Boolean
NIEOR
algebra routines, because the form of these functions is
NIAND
not defined in the F77 standard.
As for the GEN sub-directory, the SPC sub-directory should contain
the source and object files of these routines.
The remaining file is an INCLUDE file to set the system parameters.
IATSIZ - which sets the size of system wide PARAMETERs and DIMENSIONs.
The machine-type code and the sizes of all large arrays are
set in this file and it is INCLUDEd in most routines.
(See System Parameters below)
Page 18
Strictly speaking the INCLUDE statement is not part of F77, but all
compilers so far encountered have this facility in some form. The
actual INCLUDE statements in the code always refer to the file to be
INCLUDEd as a string of alphabetic characters, e.g.
INCLUDE 'IATSIZ'
and the symbol IATSIZ is made to refer to the correct file in the
particular operating system. The form of the INCLUDE statement varies
from one compiler to another, viz :-INCLUDE 'IATSIZ'
VAX VMS and SUN
INCLUDE (IATSIZ)
VM/CMS and MVS/TSO
$
INCLUDE:'IATSIZ'
MS-DOS
#include "IATSIZ"
IRIS.
There is a routine DOLLAR which can change this syntax, if necessary,
through the whole system, and it is a relatively simple matter to modify
this routine to produce the correct syntax for other operating systems.
DOLLAR can also modify all occurences of the non-standard string ,$) at
the end of FORMAT statements. In VAX F77, and many other compilers,
this string suppresses the carriage return at the end of terminal output
statements and thus allows the answer to a question to appear on the
same line as the question itself.
All plotting is now implemented in a standard way through the routine
EDRAW. Routines which use graphics are ABSORP, FOURR, COFOUR, ORTEP,
PACKER, PLTMOL and PLUTO and all routines can produce graphics for any
of the available devices. Screen graphics is oriented towards Tektronix
4000 series (or look-alike) devices and output files are produced for
hard-copy devices. At the moment the following plot files can be
produced :TK4010.PLT
TK4663.PLT
HPGL.PLT
TKLN03.PLT
TKQMS.PLT
EPSON.PLT
PROPRT.PLT
IMAGWT.PLT
PRNTRX.PLT
POSTSC.PLT
TEK 4000 series graphics commands;
Tektronix 4663 plotter commands;
HP-GL commands;
TEK 4000 commands for LN03 laser-printers with Tektronix
emulation;
TEK 4000 commands for QMS laser-printers with Tektronix
emulation;
EPSON 1050 dot-matrix printer commands;
Proprinter dot-matrix printer commands;
Imagewriter dot-matrix printer commands;
Printronix dot-matrix printer commands;
Postscript commands.
Page 19
System Parameters
----------------The [-.SPC] file IATSIZ.FOR contains PARAMETER statements which
indicate the machine type and control the size of all the large arrays
in the system. These are as follows :--MNCODE
NATSIZ
NUMPFL
NCOEFF
NCOSIZ
NCONTR
NGPADD
NGPFIL
0
All Routines
(0 VAX, 1 UNIX, 2 PC, 3/4 IBM TSO/CMS,
5 IRIS)
300 All Routines
The maximum number of atoms allowed.
600 LSTSQ
The maximum number of parameters which can be refined by the
full-matrix method. This is set to a specific value rather
than n*NATSIZ in LSTSQ to give greater flexibility. If this
number is changed remember that the matrix requires
2*NUMPFL*(NUMPFL + 1) bytes.
204000 FOURR COFOUR
The maximum number of Fourier coefficients and points allowed.
This rather odd number accomodates a wide range of the n/240
cell divisions which commonly occur.
200 COFOUR
The maximum number of points along the side of a best-plane
Fourier section.
40000 COFOUR
The maximum number of map points for contouring.
50000 DATRD2
The maximum number of unique reflections.
200000 DATRD2
The array size to hold NGPADD unique reflections.
NRETAB
50000 TABLES
The maximum number of reflections which can be processed in
one pass by TABLES.
NUMREF
1000 SOLVER
The maximum number of E-values allowed.
100 SOLVER
The maximum number of Sigma2 values per E-value.
An array 16*NUMREF*NOSIGS bytes is required by SOLVER, so
again care is required if these values are increased.
1024 SOLVER
The maximum number of phase sets.
NOSIGS
NOSETS
Any of these parameters can be changed and the appropriate routines
rebuilt with the XXMAKE.COM files, or the whole system rebuilt with the
REBUILD.COM procedure.
Page 20
Test Data
--------For a particular structure determination it is convenient to set up a
sub-directory and then all files associated with that structure are
kept together. It is the user's responsibility to clean up these subdirectories by deleting files like PEAK.DA and *.OUT which will be
created during the work. The system maintains the .CD and .RE files
automatically and most routines that use these files can read the names
from a files called NAMES.ZZ, which is written by CDFILE or can be
created with the editor. This is a two line file which contains the
.CD and .RE filenames e.g.
STRUC.CD
STRUC.RE
This prevents the annoyance of having to retype these names endlessly.
If intensity data is not collected from the NRC diffractometer
routine, it will be necessary to prepare a file in the format of the
IDATA.DA file. (Appendix 2)
A typical sequence for a structure might be as follows :-1. Get the reflection data into IDATA form
2. Run CREDUC to check the unit cell. This should have been done
before any data were collected.
3. Run SYSABS to determine (hopefully) the space-group from its
systematic absences.
4. Run CDFILE.
5. Run DATRD2 (S, R and N stages).
6. Run SOLVER using all defaults. This will probably solve the
structure
7. Run FOURR with the SOLFOU.DA phases to PEAK.DA from the E-map.
8. Run UNIMOL on PEAK.DA to get a unique molecule.
9. Run PLTMOL and write out a reasonably cleaned up molecule to .CD.
. Run CDEDIT to clean up the names etc on the .CD file.
10. Run LSTSQ for structure factors or least squares.
11. Run FOURR D-map to get more atoms if necessary.
12. Run CDEDIT to put in a few more peaks.
13. Recycle to 6.
This is by no means a hard and fast sequence and it might be
useful to try out a few routines, eg. CDFILE, CDEDIT and UNIMOL
to become more acquainted, before beginning any real structure
work.
For this purpose several sets of test data are provided.
******* COPY the test files before use in case of troubles. *******
Page 21
The first of these is the file TEST.DAT, which can be used with the
tutorial demonstration described in Appendix 12. By running the system
in conjunction with the text in the appendix a new user can carry out
a complete structure determination and refinement and in the process
learn about the system.
The second set consists of three files which are primarliy intended to
demonstrate the graphics routines PLTMOL, PACKER, PLUTO or ORTEP.
The files are
1. STRUC.CD
2. STRUC.OR1
3. STRUC.OR2
Cystal Data File.
The first of 2 Ortep drawing files.
The second Ortep file.
The third set is from one of the ruby crystals distributed at IUCr
XII in Ottawa 1981. Three files are included
1. RUBY.ID
2. RUBY.CD
3. RUBY.RE
Diffractometer intensity data file.
Crystal Data file (with atoms).
Reflection Data file.
Refer to Appendix 9 which contains sample output listings from
CDFILE, DATRD2, CDEDIT and LSTSQ for the ruby structure.
To run DATRD2 on the copy of RUBY.ID to create a reflection file, use
the following steps :1.
Run CDFILE to create a .CD file using the crystal data for ruby.
2.
Run DATRD2 using that .CD file and the copy of RUBY.ID.
Questions asked during this run should mostly be answered with
the
defaults, i.e. by typing <carriage return (CR)>. The information
needed for the remainder is given below.
a.
b.
c.
d.
The first option is 'S' to scale the data, using the NRC Picker
route with profile analysis.
The .CD file is 'RUBY.CD'.
The intensity file is 'RUBY.ID'.
Use all intensity records.
The standard numbers to be used are 1,26.
The next option is 'A' to calculate spherical absorption
corrections.
This option has already been run on the ID file, but it can be
rerun with no harm. The crystal diameter is 152 microns.
a.
b.
The next option is 'R' to reduce the data.
Two-theta(max) is 100.
Use the NRC Diffractometer Control option (#1), with profile
analysis.
The next option is 'N' for normalization and E-values.
(Note that the B-value produced is slightly negative. Ignore
it.)
The next option is 'Q' to quit and finish data reduction.
Page 22
VAX System Implementation
------------------------The system is supplied on 2400 ft, 1600 bpi magtape, written by the
VMS COPY command and labelled NRCVAX. The tape contains all the source
files, a set of command procedures to build the entire system,
documentation files, test data and a complete set of *.EXE modules.
These executable files are supplied in case of difficulties, but it is
strongly recommended that the system be totally rebuilt as explained
below. Problems have been reported in trying to run *.EXE modules
created on a 780, on other VAX machines. There is one large procedure
which uses many other procedures in the building process, and which
leaves the system in a convenient form for use and further manipulation.
There are 7 command procedures for each main routine as follows:1.
2.
3.
4.
5.
6.
7.
XXCOM.COM
XXLOAD.COM
XXMAKE.COM
XXLIST.COM
XXBACK.COM
XXCOPY.COM
XXCOPB.COM
Compile all the required subroutines
Link the subroutines
Combination of 1. and 2. above
As 1. but listings are produced & deleted
Backup all .COM and .FOR files to magnetic tape
Restore files from magnetic tape
Used by NRCBUILD.COM (see below).
These can be used to build and maintain the system. They are used by
the initial building procedure NRCBUILD.COM and also by REBUILD.COM if
the system is rebuilt after IATSIZ.FOR has been changed.
Building the system is extremely simple.
1.
Create an account, e.g. XRAY, with a disk quota of at least 20000
blocks (5000 if only the *.EXE modules are to be copied, see 4.).
2. Log on to this account and mount the magtape using the label
NRCVAX.
3. Assuming MTA0 to be the name of the magtape unit, issue the command
COPY MTA0:NRCBUILD.COM
*.*
This will copy the command procedure to build NRCVAX into the main
directory.
4. When the copy is complete the command
@NRCBUILD
will copy and run the configuration routine NRCCFG and then,
at the users discretion, either,
a. copy the test files and executable modules, which takes about
10 minutes, or
b. build the complete system, creating neccesary sub-directories
and deleting unneccesary files as it goes. This takes about
an hour even on a lightly loaded 780.
When this is finished the system is ready for use in either case.
5. Before using the system however, use the VMS editor to create a
LOGIN.COM file, from the file NRCLOGIN.COM which is in the main
directory. All routines are run directly from the operating system
prompt and the LOGIN file will simplify running each routine to a
command of 2 or 3 letters and also set up the terminal for
plotting.
Page 23
UNIX System Implementation
-------------------------The files on the diskettes
-------------------------All the files on the 4 diskettes enclosed are ASCII files which can
be printed or examined with the editor. Their functions can be
distinguished by their extensions.
Extension
Note
Kind of file
.f
Fortran
.i
(Changed to .FOR
COMMON file for inclusion
during installation)
.c
Command file pertaining to
a subdirectory
none
2 or 3 characters
Command to execute programs
name starts with 'nrc' Command relating to the
whole system
.man
Manual or notes for your info
Copying the diskettes to the hard disk
-------------------------------------The diskettes are 1.2MB, written in DOS format and they can
to the hard disk in several ways.
With MS-DOS or DOS-merge:
COPY a:*.* c:
With Unix:
doscp A:* .
[Notice the
They can also be read on an IBM PC or a clone with the COPY
above, then moved to your Unix machine using KERMIT in about 2
9600 baud.
be moved
dot]
command
hours at
These files will build a working NRCVAX system on an 80386 machine
equipped with an 80387 coprocessor and running under Microport Unix
Version V with a MicroWay NDP Fortran compiler. There are two
possible cases detailed below.
Case I: Your Unix machine is as described above
--------------------------------------1. Create a user with name nrcvax. It can in fact be called anything,
but it has to be an empty account.
2. Copy all the files from the diskettes to the main directory of the
nrcvax account.
3. Type:
chmod 777 nrcbld<CR>
( <CR> represents carriage return )
nrcbld<CR>
This will build the whole system, ready to run, in about 2 hours.
The build procedure creates directories, one for each of the 21 programs
in the system, for example $HOME/ab for the absorption program, plus
four other sub directories of $HOME: /gen, /spc, /build and /command,
and copies files to appropriate directories. The directory ab contains
the Fortran files and the command files required by the absorption
program only. The directory gen contains Fortran files required by more
than one program. All the above Fortran files are identical to those of
the VAX implementation while the directory spc contains Fortran files
that differ, usually in a trivial way from either the VAX or the IBM
version.
Page 24
The build directory contains command files to build the whole system
and the command directory contains files to run the programs from the
nrcvax account. To run them from any other account, add the statement
PATH=$PATH:/usr/nrcvax/command
to the local .profile file .
Upper case two-letter commands will work provided that the account is
called nrcvax. If the account has a different name, modify each of
these command files with the editor. The path is now modified in
your .profile file. For this modification to become effective, you must
exit then log in again. Lower case commands are also available. They
are two-letter commands except for cdf, cde, lst and tab which would
duplicate Unix commands if the corresponding two letter commands CD, ED,
LS or TA were used in lower case.
Case II: Your Unix machine is not as described above
------------------------------------------As long as you have a FORTRAN 77 compiler, the installation should
require few modifications.
1. Print the command file nrcbld which normally builds nrcvax
automatically.
2. Type in the commands until their execution produces errors.
3. Edit the command files called into execution by the typed command,
in order to find out what was wrong and correct it.
The following may be helpful.
mf77 calls the MicroWay Fortran77 compiler to compile all routines
with an extension .f, and produces objects with an extension .o,
then calls the /bin/ld standard Unix linker/loader.
-v
is the verbose switch to keep you informed.
-n2 and -n3 tell the compiler about the 80387 coprocessor. The
equivalent for the Wietek coprocessor is -n4 -n5.
-I
indicates the directory for INCLUDE files which are not in the
default directory.
a.out is the executable module produced by the linker/loader.
$HOME is the login directory, probably, but not necessarily nrcvax.
The command chmod 777 filename removes all protections, in particular
execution is allowed.
Compilation problems are unlikely to occur because this code compiles
without error with five unrelated compilers under five different
operating systems, one of them being VAX-VMS, and the execution
appears to be identical. Routines which differ between machines
are grouped in the directory $HOME/spc. These differences all
have to do with imprecision in the Fortran 77 standard giving rise
to slightly different interpretations of the code on different
machines. In case of problems, look there first.
Page 25
<CNTRL-M> characters: Conversion of files to DOS format produces
control characters at the end-of-line, which normally disappear
when files are copied back under Unix control. To delete these
control characters globally with the vi editor, type:
:%s/\<CNTRL V><CNTRL M>$//<CR>
in the command mode. <CNTRL V> means the character generated by
keeping the CNTRL key depressed while the V key is depressed once.
<CR> means the carriage return or enter key.
Running NRCVAX
-------------For details, print the file nrcvax.man which contains the manual.
Due to conflict between some nrcvax commands and Unix commands, it is
preferable to type the two-letter commands calling programs into
execution in upper case. Names of files generated by nrcvax are usually
in upper case, but the ones you specify from input can be in either
upper or lower case. With Unix, an upper case file name and a lower
case file name point at two different files.
The manual of the VAX version applies to the Unix version because the
code is the same.
Graphic programs
---------------Graphic strings for Tektronix devices are output by the Fortran
programs. They will produce pictures on Tektronix-compatible terminals,
but not on the console monitor with EGA type graphics. If you want to
do the latter, for example if you only have a console terminal, you can
install the DOS version of graphic programs and generate pictures on the
console monitor under DOS-merge. The data files can be exchanged freely
between the DOS and Unix versions because the programs are identical
apart from array sizes.
To get the DOS version of NRCVAX, send $100Can to:
Dr P.S. White, Chemistry Dept., University of New Brunswick, NB, Canada
specifying whether you prefer 360KB, 1.2MB 5"1/4 floppies or 720kB 3"1/2
diskettes.
Other distribution media
-----------------------The Unix version of NRCVAX can also be supplied on 1600bpi magnetic
tape written by a VAX. The tape can be read on other machines as well,
and then moved with KERMIT to the target machine.
Distribution of executables
--------------------------Executable modules are hardware-dependent and are not a flexible
means of software dissemination. However, if you have the configuration
of case I above, we could send executable modules on either 1.2MB
floppies or 1.4MB 3 1/2 inch diskettes.
Page 26
System Specific Routines and Non-VAX Implementation
-----------------------------------------------There are a few system specific features in the system. As described
above under System Implementation, all such features are confined to the
10 routines in the [-.SPC] subdirectory, and they have all been modified
for the UNIX, MS-DOS, VM/CMS and MVS/TSO versions. Further detail is
given below together with an indication of how to deal with them on
non-VAX machines.
The plotting routine EDRAW calls the subroutine TCROSS where there are
several system calls which return the position of the pen carriage of a
Tektronix 4663 plotter. These have now been commented out as the
facility is very rarely used. If the function is needed (for VAX only)
edit the TCROSS subroutine, which is part of EDRAW.
All other features which are likely to give trouble are connected with
input/output in some way. The assignment of I/O unit numbers is by no
means standard on different machines and the routine SETIOU deals with
this problem. On VAX computers, the standard device numbers for
terminal input and output are 5 and 6, and units 1, 2 and 3 have been
arbitrarily assigned in NRCVAX to the .CD file, the .RE file and the
lineprinter output file respectively. For non-VAX systems SETIOU.FOR
may need to be editted in order to reflect local unit numbering.
SETIOU also allows a value to be set which controls the RECL parameter
in direct-access OPEN statements. The length is specified for VAX F77
in 4-byte units and the value of the symbol IBYLEN should be 1; if the
length is specified in bytes, IBYLEN should be 4. Again, SETIOU should
be editted before the system is built.
All interactive terminal I/O is written so that the answers to
questions are given on the same line as the question. This is acheived
using the character $ at the end of a FORMAT statement. This will always
occur as the 3 character string ,$) . Some compilers will object to
this character and in this case they will have to be substituted. This
is a formidable editing task and the routine DOLLAR is supplied to help
in doing this. It runs by processing each source file in turn, from the
list of file-names contained in each file XXCOM.COM. The source code is
in the file DOLLAR.FTN, and there is a description of how to run the
routine at the head of the file. As described above DOLLAR can also
change INCLUDE statements to the syntax required by a particular
compiler.
Page 27
System Timing
------------Some typical times for different routines are as follows.
Space-group P-1, 62 atoms, 5200 reflections, 460 parameters.
VAX 11/780 with Floating Point Accelerator.
a). SOLVER 480 E-values, 37000 Sigma2 relationships.
Parts 1 & 2
6 mins
Part 3
15 secs per solution.
b). FOURR
100,000 points
(Incl. peak search)
c). LSTSQ
Full matrix method VAX
Full matrix method AP500
Blocked matrix method
2 mins
60 mins per cycle
4 mins per cycle
12 mins per cycle
Speeds relative to the VAX (1.0) for other machines are :-UNIX, 20MHz 80386/80387/Weitek 3167
4.0
Microway NDP Fortran 386
UNIX, 20MHz 80386/80387, Microway NDP Fortran 386
2.0
MS-DOS Same 80386
0.5
MS-DOS 8MHz 80286/80287
0.17
VM/CMS 3090/200S
20.0+
System Reference
---------------It would be appreciated if reference is made to the system in any
publications involving its use. The correct reference, at present,
is to the I.U.Cr.Computing School held in Mulheim F.R.G. during the
summer of 1984 as follows:
NRCVAX - An Interactive Program System for Structure Analysis
E.J.Gabe, Y.Le Page, J-P.Charland and F.L.Lee
J. Appl. Cryst. 22, 384, 1989.
Page 28
Appendix 1. Explanatory Notes for ABSORP
An absorption correction program will always require the crystal
orientation as part of its input, and for integration routines a
description of the geometry of the crystal faces. The form of this
information can vary widely with different types of diffractometer and
different methods of measuring the crystal. ABSORP is set up to accept
orientation and face information from the NRC Picker and standard CAD-4
diffractometers.
The input data needed for the empirical method are relatively simple
and will be described first, while that required for the Gaussian method
are more complex and are described in somewhat more detail.
Hopefully, the description below will enable users to adapt local
methods and conventions to the requirements of ABSORP.
Empirical Method
---------------This method only requires the orientation matrix and wavelength
values and then sets of psi-scan data (36 per reflection) for several
reflections in a data file which is usually called FCURVES.DAT. An
average correction curve is worked out and then transmission factors and
pathlength values are written to an IDATA file. The mu value is needed
in order to work out the pathlength and this is read from a .CD file.
The FCURVES.DAT file can be in one of two forms.
1. For a CAD-4 diffractometer this file can be in the normal intensity
data file format and either the standard E-N or NRCCAD form is
acceptable.
2. For a Picker or any other diffractometer data it can be an ASCII
file similar to the CAD-4 file as follows :-1st line - Type 31 with 7 values
31
R(1,1) R(1,2) R(1,3) R(2,1) R(2,2) R(2,3)
2nd line - Type 32 with 4 values
32
R(3,1) R(3,2) R(3,3) Wavelength
Remaining lines - Type 1 with 10 values
1
h k l Psi Frac IBlow IPeak IBhigh IAtten
where Frac
is half the ratio of the total background time to the
peak time, i.e. 0.5*(Tblow + Tbhigh)/Tpeak.
IAtten is the index of any attenuators (0 to 5).
Gaussian Integration Method
--------------------------Crystal Orientation
------------------The crystal orientation is described in terms of an orientation
matrix or the angles required to bring three reflections to the
diffracting position. Unfortunately, there is no agreement among
diffractometer manufacturers on a convention for the description of the
orienting angles and apart from this, there are of course the two
different orienter geometries in common use. ABSORP is set up to accept
orientation input as a matrix or Euler angles from the NRC Picker and
Page 29
CAD-4 diffractometers. In order for this to be of use to other users the
angle convention of the NRC Picker machine is described. CAD-4 users
can use data direct from the CAD-4 or NRCCAD control routines.
On the NRC Picker machine, viewing the chi-circle from the X-ray tube,
with all angles set to zero, chi=0 is at the bottom and chi=90 is to the
right; i.e. from this viewpoint, when the chi angle increases it does so
by moving clockwise. The phi-circle is at the bottom of the chi-circle
when chi=0, and phi=0 points towards the viewer, with phi=90 to the
right. This means that viewing vertically downwards from the crystal
position, phi also increases in a clockwise sense. The two Picker face
data files shown below contain the matrix and angle description of the
same crystal orientation on the NRC Picker machine. With all angles at
zero, as above, the goniometer head, locating pin on the phi-circle base
is at phi=160. (See Delta below)
When using a CAD-4 machine we have found it useful, though not
essential, to know the conversion of the CAD-4 matrix or angles to NRC
Picker form. Assuming the angles on all CAD-4 diffractometers are defined
in the same way (this was not true for Picker machines !), the relevant
conversions are as follows.
Phi(NRC-Picker) = Phi(CAD-4) + 180.0 + Delta
Chi(NRC-Picker) = -Chi(CAD-4)
On our CAD-4, with all angles set to zero the locating pin points
directly at the x-ray tube. This means that the phi transformation is
Phi(NRC-Picker) =
i.e. delta = -20.0.
Phi(CAD-4) + 180.0 - 20.0
The CAD-4 routines store their orientation matrix in a different row
order to the NRC routines, and this coupled with the angle definitions
above means that if Rp(3,3) is the orientation matrix for the NRC-Picker
machine (with the zero position of phi set to read 20 degrees), the CAD-4
matrix Rn(3,3) is
Rn(3,3)
=
Rp(2,1)
-Rp(1,1)
-Rp(3,1)
Rp(2,2)
-Rp(1,2)
-Rp(3,2)
Rp(2,3)
-Rp(1,3)
-Rp(3,3)
The two CAD-4 face data files below, contain the description of the
same crystal as above, but in CAD-4 terms. Note that theta is given in
place of 2theta, and chi and phi are interchanged, to match CAD-4
output. Note also the 20 degree shift of phi.
Face Description
---------------The orientation of faces is described to ABSORP in terms of the Euler
angles required to put each face in the diffracting position or its
reverse, for bisecting geometry on a 4-circle instrument. On the Picker
machine this means that the face normal is in the horizontal plane,
pointing at the chi-ring and the standard Picker microscope is viewing
the trace of the face. In fact, it is very convenient to use a Picker
diffractometer to measure crystals in this way, because of the ability
Page 30
to unlock the drive mechanisms and spin the circles by hand. The same
operation can be done on a CAD-4 with the commands MICROS, MICROR and
HE, but it is tedious. It helps considerably if the faces can be
indexed and there is provision for face input in the form h,k,l,d. The
measurements can be made quite conveniently on a 2-circle optical
goniometer and the results transformed to Picker values for input. If
face data is specified as h,k,l,d, it is permissible, though perhaps not
advisable, to mix h,k,l and angle input for different faces. It is also
advisable to use the B setting in this case to avoid confusion.
In addition to the angles required to orient the face in this way, the
distance from the face to the centre of the crystal (which should be the
centre of rotation), along the face normal, is required. For symmetric
crystals this is not difficult to measure, but for irregular crystals it
requires some practice. If the faces can be indexed, then the angles can
be easily calculated, but as the faces of many crystals cannot be easily
indexed, it is more comprehensive to give the face data in angular form.
In any case, it is still necessary to measure the perpendicular distance.
--------------------------Crystal orientation and face data for ABSORP must be in a consistent
form. The values given can be for a Picker or Nonius diffractometer, but
they must be consistent.
--------------------------A final word of explanation is required to describe the orientation of
the crystal drawings produced by ABSORP. The graphics axial system is
fixed in space with y along the x-ray beam pointing to the right of the
screen, z vertically upwards and x outwards towards the viewer. The
initial view of the crystal, is at it would appear on the Picker
machine, looking down the x-axis, i.e. the diffraction vector, towards
the origin with all diffractometer angles set to zero. Rotations are
clockwise when looking from a positive axial direction towards the
origin.
The face data in the examples is for a tetrahedral crystal mounted
with its base vertical. For the data in example 1 this means that the
initial view is that which would be obtained by looking through the
metal of the chi-circle at the base of the crystal (face 1), with face
2 downwards, face 3 to the left and face 4 to the right. In this
orientation the crystal would be mounted on face 2. As the Picker
microscope is mounted at right angles to the chi-circle and away from
the x-ray tube, the view in the microscope can be obtained byrotating
the crystal image 90 degrees about z.
---------------------------ABSORP Face Data File Examples
The four files shown below contain examples of orientation and face
information, which can be used as input to ABSORP. The same data can be
given at the terminal in response to prompts and the program will then
write the face data file automatically. The contents of these files is
Page 31
as follows.
Line 1
Wave,Idiff,Imat,Iface (F10.0,3A1)
Wave
Wavelength used (in Angstroms),
Idiff Diffractometer flag; P=NRC Picker,
N=Nonius CAD4
Imat
Matrix input flag;
M=Matrix input, A=Angle input
Iface Face data flag;
B=Bisecting,
R=Reverse of B
Lines
2,3,4
If
If
Line 5
a,b,c,alpha,beta,gamma. (For checking purposes only)
Line 6
Mu,Igx,Igy,Igz,Nface.
Mu is the absorption factor in cm-1,
Igx,Igy,Igz are the no. of integration pts along x,y,z,
Nface is the number of crystal faces.
Line 7
If
If
Imat=M
Imat=A
Idiff=P
Idiff=N
Orientation matrix from diffractometer
h,k,l,angles for 3 reflections
If Idiff=P angles are 2theta,chi,phi
If Idiff=N
"
"
theta,phi,chi
chi, phi, d(in cms) for each face.
phi, chi, d(in cms) for each face.
If Iface=B The chi and phi values needed are those which
will put the face in the normal position for
reflection in the bisecting mode.
If Iface=R The chi and phi values are the reverse of those
above. thus if phi and chi are the normal
angles used for Iface=B, then these angles are
phi' = phi + 180 and chi' = 360 - chi
Example 1.
ABSORP Input File for the Picker machine, with
orientation specified as reflection Angles and faces
specified for the Bisecting position.
0.709320PAB
6
0
0
31.500
318.080
256.850
0
6
0
31.500
3.120
300.450
0
0
12
37.490
323.120
27.790
9.06000
9.06000 13.24400
90.000
90.000
50.0000
20
20
20
4
0.000
0.000 0.020000
60.000
180.000 0.020000
-30.000
120.000 0.020000
-30.000
240.000 0.020000
Example 2.
120.000
ABSORP Input File for the Picker machine, with
orientation specified as reflection Matrix and faces
specified for the Bisecting position.
0.709320PMB
-0.021660 0.064440
-0.092680 -0.109600
0.053460
0.028220
Page 32
-0.085220
9.06000
50.0000
0.000
60.000
-30.000
-30.000
Example 3.
0.007100 -0.045230
9.06000 13.24400
20
20
20
4
0.000 0.020000
180.000 0.020000
120.000 0.020000
240.000 0.020000
90.000
90.000
ABSORP Input File for the Nonius CAD-4 machine, with
orientation specified as reflection Angles and faces
specified for the Bisecting position.
0.709320NAB
6
0
0
15.720
96.890
41.510
0
6
0
15.720
140.430
-3.620
0
0
12
18.740 -132.250
36.480
9.06000
9.06000 13.24400
90.000
90.000
50.0000
20
20
20
4
200.000
0.000 0.020000
20.000
-60.000 0.020000
320.000
30.000 0.020000
80.000
30.000 0.020000
Example 4.
120.000
120.000
ABSORP Input File for the Nonius CAD-4 machine, with
orientation specified as reflection Matrix and faces
specified for the Bisecting position.
0.709320NMB
-0.094655 -0.080945 0.044930
-0.011438 -0.097950 -0.040811
0.084383 -0.008039 0.044881
9.06000
9.06000 13.24400
50.0000
20
20
20
4
200.000
0.000 0.020000
20.000
-60.000 0.020000
320.000
30.000 0.020000
80.000
30.000 0.020000
90.000
90.000
120.000
------------------------------------------------------
Because the Gaussian calculations for ABSORP can take an appreciable
length of time to run, it is often preferable to run it as a batch job.
The file below is a simple VAX DCL command procedure to do this, which
should be run from the main directory.
$ !
File to run ABSORP as a batch job (ABATCH.COM)
$
$
$
$
$
!
! Force the LOG file to be kept on ABATCH.LOG
DEFINE SYS$PRINT DUMMY
!
! The next few lines describe the terminal input to ABSORP, which must
Page 33
$ ! be included in the file for the batch job.
!
! Let the ABSORP routine know its a BATCH job
$
TESTBATCH := "YES"
!
! The next few lines are a description of the terminal input
!
! 1. 'G' to use the Gaussian method
! 2. 'Y' to run as a BATCH job
! 3. 'T' for output to terminal
! 4. Name of the FACE DATA file
! 5. 'Y' to use an INTENSITY DATA file
! 6. Name of the INTENSITY DATA file
! 7. Either
!
'Y' to use all data blocks, or
!
Up to 10 ranges of data block numbers (End with 0)
!
$ R ['TOPDIR']ABSORP
g
y
t
[GABE.ab]face.da
y
[GABE.em]test.id
n
20,100
0
$ EXIT
Page 34
Appendix 2.
Explanatory Notes for DATRD2
The data reduction routine, DATRD2, processes intensity data in
standard NRCVAX IDATA form to produce a reflection (.RE) file.
Intensity data from the NRC Picker diffractometer, a standard Picker
diffractometer, a standard CAD4 diffractometer, the NRCCAD control
program or from any of the foreign data conversion routines in UTILTY,
can be processed.
The form of the input intensity data is as produced from the NRC
Picker program and is described later in this Appendix. The routine
NONIUS in UTILTY will convert CAD4 intensity files into the required
form. The routines NICLAY (Nicolet), PHILPS (Philips), RIGAKU (Rigaku),
FINGER (Finger), LENHRT (Lenhert), IUCIN (I.U.Cr.) and REFIN (General),
all of which are in UTILTY, will perform the necessary conversion for
various other forms of nonstandard data.
The program needs two input files and produces two output files. The
two input files are a .CD file and an IDATA file. The main output file
is the .RE reflection file and there is also a lineprinter output file,
DATRD2.OUT, which gives summaries of the results of the various program
steps.
DATRD2 performs 5 data reduction steps, which are accessed via key
letters from within the program.
1. E
Examine and edit the raw intensity data on the IDATA file. Data
blocks or individual reflections can be examined and changed
prior to the calculation steps of the program. This stage is
menu-driven from the terminal and should be easy to run.
2. S
Scale the measurements according to one of several options, from
the standard reflection measurements on the IDATA file. The user
must supply the routine with the type of data being processed
and the range of blocks to be considered. The routine then
searches these blocks for standard reflection measurements and
plots the values of each on the screen. It then asks which
standards should be used and whether any data should be omitted.
The mean standard value is then plotted and the scaling option
is asked for. There are 4 such options :-1. Use the scale value of the last set of standards measured.
2. Apply an average constant scale to specified sections of
data.
3. Apply interpolated least squares straight line fits to the
standard measurements in sections of the data.
4. Apply the running 5-point smoothed value of the scale to
sections of the data.
The derived scale values are again plotted and, if acceptable,
scale values are written in each data block.
3. A
Apply spherical absorption corrections. Values of the spherical
transmission correction and average pathlength through the
crystal are written in each reflection record if this option is
Page 35
selected, using the calculated absorption coefficient and stored
correction tables. (Weber, Acta Cryst., B25, 1174,1969; Larson,
Crystallographic Computing, p.293, 1969)
4. R
This step is performed in two stages.
a. Equivalent reflections are grouped together.
b. The grouped data is reduced to Fobs values.
a. Group equivalent measurements together for subsequent averaging
This step must be run even if there is only one unique
measurement of each reflection. The algorithm for this step is
based on the use of Dh segments as defined in Le Page and Gabe,
J. Appl. Cryst., 12, 464, 1979. The program works out a unique
reflection address in the array GPFILE, based on the symmetry
of the problem at hand and the number of equivalent measurements.
The address of each reflection record in this array is worked
out from stored segment data for each symmetry and enough space
is reserved for each reflection to hold data for all equivalents
(including Friedel) in each unique reflection record. At the end
of this step the GPFILE array holds all the intensity data
sorted according to unique reflection indices.
b. Reduce the raw data to Fo and weight values and write the .RE
reflection file. Once the GPFILE array has been created it is
a relatively simple process to apply the necessary geometric
and physical corections to produce a unique set of averaged
values of Fo and weights based on counting statistics or
interset agreement statistics, if there are several equivalent
sets. The reflection file can be written in any required order.
Agreement statistics are kept during this process and output to
the lineprinter file. Measurements are screened for consistency
during this stage if there are 4 or more equivalents. A
reflection whose intensity differs from the mean by more than 4
times the mean counting statistics sigma is dropped and the mean
recalculated. The process is repeated as long as not more than 1
measurement in 4 has been rejected. A secondary extinction
correction is calculated according to Zachariasen, Acta Cryst.,
23, 558, 1967 and Larson as above.
5. N
Normalize the scattering data to produce E and Epsilon values.
Statistics are accumulated from the .RE file, a scale value and
average temperature factor are calculated and E-values written
to the .RE file. A summary is output to the lineprinter file.
All reflection data, from whatever source, is input to DATRD2 as
unprocessed intensity data in an IDATA file, where it is processed to
yield a .RE file. The IDATA file is a direct-access binary file in which
each record is 340 bytes long, i.e. 85 4-byte variables. Intensity data
storage starts at record 20.
Eight quantities are stored for up to 10 reflections as follows:-10 values of 1000(h + 500) + k + 500
10
"
" 1000(l + 500) + ia (attenuator index, 0 to 5)
Page 36
10
10
10
10
10
10
"
"
"
"
"
"
"
"
"
"
"
"
the integrated peak count
" low angle background count
" high "
"
"
" background time fraction
" reflection sequence number
psi, the azimuthal angle
The first (h,k) and second (l,ia) sets of values are integers and the
remainder are floating point. The time spent on background counting at
each end of the scan is expressed as a fraction of the time spent on the
peak, ie. a value of 0.236 means that each background was measured for
0.236 of the peak time. This is to accomodate the variable background
times produced by he profile analysis routine. For reference
reflections the values of psi are set to 999.0. Records which do not
contain 10 reflections are filled with h=k=l=99 ie. 599599 and 599000.
The routine ABSORP writes the transmission factors in the sequence
number array and beta values in the high angle background array. The two
backgrounds are added prior to this of course, and ABSORP adds 10000 to
psi to prevent this happening again if ABSORP is run a second time.
Data from all sources must be converted into this format by the
appropriate routine in UTILTY.
The NONIUS routine processes intensity data from the regular CAD-4
program and the NRCCAD program, which may use profile analysis.
Data from Nicolet and Philips diffractometers and Lenhert's and
Finger's systems can be transformed by special routines in UTILTY and
the routine IUCIN will convert reflection data in I.U.Cr. standard form.
Data from other instruments must also be converted in this way and
the routine REFIN in UTILTY will do this for many non-standard
reflection data types. This routine has 3 running modes. In all modes
the reflection data must be on file as 1 reflection per line, but the
individual items, h,k,l,Fobs or Inet or Peak etc may be in any field
position on the line, which must be indicated during the initial
terminal dialogue. The data is read by a free-format routine in which
extraneous alphanumeric characters are rejected. Field delimiters can
be blanks or commas.
1. Fobs Mode
In this mode reflection data is in the form of h,k,l,Fobs and
optionally a sigma(Fobs) quantity. In this mode a .CD file must
be prepared before the run, in order to supply the values needed
for the Lp-1 calculation to reconstruct the measured intensity.
The Lp-1 expression used is for monochromatized radiation of the
selected wavelength, with the reflecting planes of the
monochromator perpendicular to those of the sample crystal
(Picker and CAD-4 geometry). The sigma quantity may be 1 of 8 forms
which are indicated in the routine.
2. Inet Mode
In this mode the data is in the form h,k,l,Inet, an optional
sigma(Inet) and an optional reference reflection indicator flag.
The reference reflection indicator can be any selected non-numeric
character (usually *), which can occur anywhere on the line. Usually
this will be at the beginning or the end and it does not require its
own field, i.e. it can occur alone, it does not need delimiters.
The same general rules apply and sigma may be 1 of 4 different
Page 37
expressions.
3. Peak/Background Mode
This is the most general mode of the program. Data is in the form
of h,k,l, a peak measurement, one or two background measurements,
some value to indicate the peak/background time ratio (see below),
an optional attenuator index and an optional reference reflection
indicator as above.
The time ratio information may be given in several ways.
a) As a constant backgound time from the terminal, in which case
there must be a variable peak-time for each reflection on file.
b) As a fixed backgound-to-peak time ratio at the terminal.
c) As a variable background-to-peak time ratio on file.
The attenuator index information is given as a number in the range
0 to 5.
If you are in doubt about any of this consult the program listings.
The relevant routines are REFIN, REFOBS, REINET and REBPKB in [*.UT].
If a local absorption routine is to be used, it may be preferable
to modify it so that intensity data (with transmission factors) are
written out as in ABSORP. The file is essentially an IDATA file
as above, i.e. direct-access, 85-variables/record, and records
1 to 19 are ignored.
The quantities written out from ABSORP are
KH
10 values of 1000(h + 500) + k + 500
LA
10
"
" 1000(l + 500) + ia (attenuator index, 0 to 5)
PK
10
"
" the integrated peak count
BKG 10
"
"
" total background count (b1 + b2)
BETA 10
"
"
" average reflection pathlength
T
10
"
"
" background time fraction (as above)
ABC 10
"
"
" transmission factor
PS
10
"
" 10000 + the azimuthal angle psi (usually 0 or 999).
If the absorption routine does not calculate BETA, substitute
a reasonable value (50-150), as a number of microns.
When an IDATA file is prepared in either of these formats the
questions in DATRD2 should be answered as if the NRC diffractometer
routine was used to collect the data, and profile analysis was
used. For data from the regular CAD4 or NRCCAD programs answer the
DATRD2 questions appropriately for those forms.
Page 38
Appendix 3.
Explanatory Notes for Multan80 with NRCVAX
The complete Multan-80 package of programs contains 4 routines -NORMAL, MULTAN, EXFFT and SEARCH. The package has been implemented for
the NRCVAX package with no change to the code, and
because of this the routines are not as interactive as others in the
system. Only NORMAL and MULTAN are included and links into
and out of these two routines are provided. The subroutine M8XIN in
UTILTY
takes data from a pair of files, .CD and .RE, and writes an input file,
NORM80.CDR, as input for NORM80'. NORM80 and MLTN80 may then be run,
followed by the routine M8XOUT in UTILTY which writes the phase
information into a file called SOLFOU.DA in a form suitable for input
to FOURR. From that point the normal NRCVAX sequence can be resumed.
The procedure M80RUN.COM (listed below) will perform this sequence of
operations automatically on a VAX.
$ ! M80RUN.COM
Command file to run Norm80 and Mltn80
8-May-89
$ !
$ WRITE SYS$OUTPUT "
Procedure to run NORM80 and MLTN80"
$ ! Norm80 and Mltn80 are in their original condition and can be run
with
$ ! this procedure as one continuous run. The input file to Norm80 is
$ ! prepared from a .CD and a .RE file, whose names must be in NAMES.ZZ.
$ ! A title file MLTN80.TTL is prepared by this procedure and
$ ! contains a title line followed by one blank line.
$ !
$ INQUIRE TITLE " Type a title "
$ OPEN/WRITE UNIT MLTN80.TTL
$ WRITE UNIT TITLE
$ WRITE UNIT " "
$ CLOSE UNIT
$ !
$ ! All terminal input is contained in this procedure
$ !
*** DO NOT ATTEMPT TO TYPE ANYTHING MORE DURING EXECUTION ***
$ !
$ WRITE SYS$OUTPUT " "
$ WRITE SYS$OUTPUT " *** Do NOT type anything more during execution ***"
$ !
$ ! The procedure executes the following steps
$ !
1. Runs M8XIN to make the file NORM80.CDR from .CD and .RE files.
$ !
2. Runs NORM80
$ !
3. Runs MLTN80
$ !
4. Runs M8XOUT to make the file SOLFOU.DA for FOURR
$ !
$ ! It is probably most useful to execute the procedure from the sub$ ! directory containing the .CD and .RE files of a particular
structure.
$ ! The procedure itself can be stored in the main directory. The symbol
$
$
$
$
$
$
$
$
!
!
!
!
!
!
!
!
TOPDIR must be defined as in NRCLOGIN.COM to be the directory which
contains the executable program modules.
If the procedure ends abnormally give the following two commands to
reassign terminal I/O correctly
ASSIGN SYS$INPUT FOR005
ASSIGN SYS$OUTPUT FOR006
Run M8XIN from UTILTY to produce NORM80.CDR
Page 39
$ WRITE SYS$OUTPUT " "
$ WRITE SYS$OUTPUT " Starting M8XIN"
$ R ['TOPDIR']UTILTY
3A
80
Y
Y
$ !
Run NORM80
$ ! The file NORM80.CDR is read by NORM80 on unit 5 (FOR005)
$ ! Any optional input to NORM80 may be editted into NORM80.CDR
$ ! Lineprinter output from NORM80 is produced on unit 6 (FOR006)
$ ! The transfer file from NORM80 to MLTN80 is on unit 9
$ ASSIGN NORM80.CDR FOR005
$ ASSIGN NORM80.OUT FOR006
$ WRITE SYS$OUTPUT " "
$ WRITE SYS$OUTPUT " Finished M8XIN; starting NORM80"
$ R ['TOPDIR']NORM80
$ ! Activate the next statement to print NORM80.OUT
$ ! PRINT/DEL NORM80.OUT
$ !
$ !
Run MLTN80
$ ! The title file MLTN80.TTL is read by MLTN80 on unit 5 (FOR005)
$ ! Any optional input to MLTN80 can be included in MLTN80.TTL
$ ! Lineprinter output from MLTN80 is produced on unit 6 (FOR006)
$ ! Binary phase information is output from MLTN80 on unit 10
$ ASSIGN MLTN80.TTL FOR005
$ ASSIGN MLTN80.OUT FOR006
$ WRITE SYS$OUTPUT " "
$ WRITE SYS$OUTPUT " Finished NORM80; starting MLTN80"
$ R ['TOPDIR']MLTN80
$ ! Activate the next statement to print the results in MLTN80.OUT
$ ! PRINT/DEL MLTN80.OUT
$ !
$ ! Run M8XOUT from UTILTY to produce SOLFOU.DA for FOURR
$ ! Assign Fortran units 5 and 6 back to their normal values
$ ASSIGN SYS$INPUT FOR005
$ ASSIGN SYS$OUTPUT FOR006
$ WRITE SYS$OUTPUT " "
$ WRITE SYS$OUTPUT " Finished MLTN80; starting M8XOUT"
$ R ['TOPDIR']UTILTY
3B
$ !
$ ! The file SOLFOU.DA now contains the phase information for FOURR
$ WRITE SYS$OUTPUT " "
$ WRITE SYS$OUTPUT "
*** Normal Completion ofM80RUN ***"
$ WRITE SYS$OUTPUT "
NORM80 results are in NORM80.OUT"
$ WRITE SYS$OUTPUT "
MLTN80 results are in MLTN80.OUT"
$ WRITE SYS$OUTPUT "
Phase Information for FOURR is in SOLFOU.DA"
$ ! Clean up the scratch files
$ DEL FOR0*.DAT;*
$ EXIT
Page 40
Appendix 4.
Explanatory Notes for CDEDIT
This program is designed to modify the preliminary data parameters
and flags for such things as the extinction and reflection scale
factors and to insert, delete and modify atom records in a .CD file,
or examine .CD files without change. All data on the file is stored
in memory until the last step of the run when it is written to the
output file after requesting the name of this file. If an existing
file is used its contents are overwritten by the new data.
The program is highly interactive and it is hoped that the prompt
questions asked are sufficiently self-explanatory that it can be
run easily by all users. Wherever possible answers to questions are
defaulted, so that merely typing CR (Carriage Return) will cause
the required action. The default answer is always indicated by (Y)
or (N) before the question mark. the program is menu driven and the
current menu can be displayed at all times merely by typing CR in
response to the command prompting question.
All numerical data used in this program is read as an 18A4 array
and then decoded by the subroutine CDFLOT which can interpret
rational fractions. It will catch illegal characters in the data
string and the program then repeats its request for data. In general
all number fields are 15 characters long unless terminated with a comma
or a space. Leading spaces are counted as part of the number field,
but a trailing blank terminates the number.
The following is an explanation of the program and its prompting
questions. The questions are shown in capital letters and the explanatory
text is in small letters.
1)
PRINT OUTPUT ON TERMINAL OR LINEPRINTER (T) ?
Select the output device to be the lineprinter file or the
terminal.
If the lineprinter is selected output will be to the file
CDEDIT.OUT.
2)
The name of the .CD file to be used is then printed (if there is a
NAMES.ZZ file). This file may be used or another.
Preliminary Data Editting
------------------------The preliminary information on the .CD file is then printed, followed
by the question
4) DO THESE DATA NEED EDITTING (N) ?
If the answer is N go to Q. 20
If the answer is Y the following options are available :-(F) New Fobs-scale
(X) New Extinction
Q. 5
Q. 6
Page 41
(R) Change refinement flags on scale & extinction
(C) Change the chirality parameter eta and its
refinement flag.
(L) List current preliminary parameters
(I) Change the instrumental error factor
(W) Change the weighting scheme flag
(A) Change the sign of anomalous dispersion terms
(E) Exit to next step
QS 7 & 8
Q. 8a
Q. 9
QS 10-13
Q. 20
If the character typed is not in the above list the full menu of
permissible values is listed with a repeat of Q. 4. This is true
of all menus in the program.
5)
6)
7)
8)
8a)
9)
10)
11)
12)
13)
NEW FOBS-SCALE ?
NEW EXTINCTION COEFFICIENT ?
REFINE FOBS-SCALE (Y) ?
REFINE EXTINCTION (N) ?
THE PRESENT ETA VALUE IS X.XXX. TYPE THE NEW VALUE
REFINE THE CHIRALITY PARAMETER ETA (N)
These questions will not appear if the space is centrosymmetric
and refinement of eta is not allowed in this case. Refined values
close to + or -1 are to be expected. If a value of -1 is found,
use the UTILTY routine MINUS to reverse x,y,z and set eta to +1.
THE INSTRUMENTAL ERROR FACTOR IS X.XX...
TYPE THE NEW VALUE
This is the value of k in the weight expression
wt 1.0/(sigma(Fobs)**2 + k*Fobs**2)
(C) COUNTING STATS, (U) UNIT,(H) HUGHES WTS ?
If H answer questions 11-13
HUGHES WEIGHTS CUTOFF ?
A & B FOR DATA > CUTOFF
A & B FOR DATA < CUTOFF
Overall Atoms Editting Options
-----------------------------The program then prints
XX ATOMS HAVE BEEN READ IN
followed by the question
20) OVERALL ATOMS EDITTING OPTION (MENU) ?
(E) Edit an atom record.
(D) Delete an atom
(I) Insert an atom
(L) List a range of atoms
(R or P) Read atom positions from a PEAK file
(A or T) Read atom positions from a TEXT file
QS. 21-31
Q. 21
QS 35-40
QS 45-47
QS 45-46
(H)
(N)
(G)
(0)
(F)
Generate hydrogen positions from .CD file data
Normalize X....H-atom bond lengths
Edit atom parameters globally by type or atom#
Order the atom entries in the file
Finish and write the atom records to the .CD file
QS
QS
QS
Q.
QS
51-56
57-59
60-69
70
75-78
Page 42
(C) Calculate symmetry constraints for all atoms.
(Q) Quit. End the job without rewriting the .CD file.
(C) Generate CONSTRAINED Groups and Atoms
QS 80-88
21)
ATOM NAME ?
The routine allows 3 tries before returning to Q. 20
22)
INDIVIDUAL ATOM EDIT OPTION (MENU) ?
(P or L) Print(List) atom data
(X) Change x, y, z, occupancy
(A) Convert iso to aniso
(U) Change thermal parameters
(M) Modify the refinement flags
(I) Change the atom identity (name)
(T) Change the atom type flag
(D) Change the anomalous dispersion flag
(O) Change the site occupancy
(N) Select the next atom to process
(E) Exit from the atom edit mode to Q. 20
Q. 23
QS
Q.
Q.
Q.
24-26
27
28
29
Q. 30
Q. 31
Individual Atom Editting Options
-------------------------------23)
24)
25)
26)
27)
28)
NEW X, Y, Z, OCCPY (1.0) ?
If the occupancy is 1.0 it need not be typed.
All quantities may be typed as rational fractions if desired.
ISOTROPIC OR ANISOTROPIC (I) ?
ISOTROPIC U (0.04) ?
ANISOTROPIC UIJS
CURRENTLY REFINABLE PARAMETERS ARE .....
WHICH PARAMETER REFINEMENT FLAGS DO YOU WISH TO CHANGE ?
Refinement flags are O,X,Y,Z and U. The presence of the letter
means the associated parameter will be refined and the sense of
the flag will be reversed by typing the letter, e.g. after O-Y-U
appears, typing OXYZU will give -X-Z-.
G may be substituted for O if desired.
NEW ATOM I.D.
The new name cannot be same as one currently in the file. If many
of the atoms on the file are to be renamed it is preferable to
use
29)
30)
31)
the routine NUNAME in the program UTILTY.
NEW ATOM TYPE ?
NEW SITE OCCUPANCY ?
ATOM NAME (Q. 21)
Insert a New Atom Record at the End of the List
-----------------------------------------------
35)
36)
37)
38)
39)
ATOM NAME ?
Cannot duplicate a name already in the file.
ATOM TYPE ?
X, Y, Z, OCCPY (1.0) ?
ISOTROPIC OR ANISOTROPIC (I) ?
ISOTROPIC U (0.04) ?
(as Q. 23)
(as Q. 24)
(as Q. 25)
Page 43
40)
ANISOTROPIC UIJS
(as Q. 26)
Select Peak Positions from a Fourier Peak File.
----------------------------------------------If many peaks are to be taken from the peak file it is simpler
to use the program UNUMOL to read them into the .CD file.
45)
46)
47)
READ ATOM PARAMETERS FROM AN EXTERNAL FILE
TYPE THE NAME OF THE FILE (PEAK.DA)
The Fourier program produces a PEAK.DA file or a similar file
can be prepared by hand, or, files similar to those produced by
TABLES can be read. The atom name must be in the first 10 places
followed by x,y,z and Biso. Esds in brackets after each
quantity are interpreted, but may be omitted.
SPECIFY THE RANGE OF ATOM NUMBERS TO BE READ AS N1,N2
If N1 = 0 Return to the OVERALL atoms edit menu
If N2 = 0 N2 = N1
These are the atom numbers on the external file.
ENTER THE DEFAULT ATOM TYPE (C)
Give the scattering factor type for all atoms taken from a PEAK
file, i.e. if this option is selected with R or P. If it is
selected with A or T, the atom type is derived from the first 1
or 2 letters of the atom name, which must therefore be a valid
atom symbol for an atom type which is in the .CD file. If the
derived symbol cannot be found the correct symbol is requested.
Hydrogen Atom Position Generation
---------------------------------
51)
52)
53)
54)
55)
THERE ARE FOUR TYPES OF H-ATOM GENERATION
2 H-ATOMS AB---X--H2
METHYLENE
(M)
1 H-ATOM AB---X--H
PLANAR
(P)
1 H-ATOM ABC---X--H
TETRAHEDRAL (T)
1 H-ATOM A(BC)---Y---X--H ORIENTED
(O)
For the O option X--H is parallel to A( or B or C)---Y.
WARNING *** RUN UNIMOL BEFORE THIS OPTION
TYPE THE ATOM--H DISTANCE (1.08)
The default value is 1.08A
TYPE AN ATOM NAME
Type the name of the atom to which H-atom(s) are to be attached.
Typing a blank causes a return to Q. 20
ENTER TYPE OF H POSITION(S) WANTED (M,P,T OR O)
At this point a hydrogen position is printed
TYPE A NAME FOR THIS HYDROGEN (Made up name)
The name for the generated H-atom is made up from the atom name
and it will be used as the default.
56)
At this point the second H position is printed (M) or Q. 53 or
for the O option,
GENERATE FURTHER H-ATOMS WITH THE M OR P OTIONS (Y)
A judicious use of this command, coupled with UNIMOL, should be able
Page 44
to generate H-atom positions for almost any geometry. For example, for
the pi-allyl group H2C---CH---CH2, which is planar with all angles 120
degrees, can be dealt with as follows. Run UNIMOL with a low specific
radius limit on any atoms bonded to the central C except the 2 other
C-atoms in the group, which should yield only 2 bonds to the central C
atom. Position the central H-atom with the P option, then 2 of the
terminal H-atoms (one on each C) with the O option using the central
C--H as the orienting bond, then position the remaining 2 terminal
H-atoms with P options.
Hydrogen Atom Bond Normalization
-------------------------------This option allows the user to normalize bond lengths involving
H-atoms which often become unreasonable during refinement.
57)
58)
59)
As 52) and then 53).
If the atom specified has only 1 H-atom attached the bond length
is normalized to the distance given in 52).
If the atom has more than 1 h-atom attached, the bond length of
the H-atom specified is normalized. This may be repeated until
all lengths have been normalized.
Global Edit Options
-------------------
Atom records can be edited globally by atom type or by ranges of
atom numbers in the list. Specified changes are then made to all
selected atoms.
60)
EDIT BY ATOM NO. RANGES (Y) ?
(Q. 62 IF
61)
62)
63)
ENTER UP TO 10 RANGES EXIT WITH CR
ATOM TYPE FOR EDITING ?
GLOBAL ATOMS EDIT OPTIONS (MENU) ?
A Convert iso to aniso
I Set iso U
U Convert aniso to iso
M Modify the refinement flags
O Shift the origin
S Select another atom type or atom# to process
N Change atom name from peak# to xxxx#
T Set atom type
D Change the anom. dispersion flag
G Global atom delete
B Add a character at the 5th place of an atom name
C Change the atom occupancy factors
E Exit to atoms editting option at Q. 20
ISOTROPIC U (0.04) ?
THE REFINABLE PARAMETERS ARE OXYZU
(to Q. 63)
N)
64)
65)
(Q. 64)
(Q.
(Q.
(Q.
(Q.
(Q.
65)
66)
60)
67)
62)
(Q. 68)
(Q. 69)
66)
67)
68)
69)
WHICH PARAMETER REFINEMENT FLAGS DO YOU WISH TO CHANGE ?
(As for Q. 27. The specified changes apply to all selected atoms)
X,Y,Z OF NEW ORIGIN, Xnew Xold - Xorigin ?
NAME WANTED INSTEAD OF PEAK
TYPE THE CHARACTER YOU WANT TO ADD
ATOMS OCCUPANCY FACTOR
Page 45
Reordering Atoms on a .Cdfile
----------------------------70)
THE ATOM WHOSE NAME IS GIVEN FIRST WILL BE PUT AHEAD
OF THE ATOM WHOSE NAME IS GIVEN SECOND.
<CR> FOR THE 1ST NAME EXITS FROM THE LOOP
<CR> FOR THE 2ND NAME PUTS THE 1ST ATOM AT THE END.
This is the simplest way to reorder a whole file.
Normal Exit from the Program.
-----------------------------
75)
OUTPUT FILE NAME (INPUT FILE)
CR means that the old .CD file will be overwritten with the
new information and is the usual exit route.
76)
ALL ATOMS SHOULD BE MADE ANOMALOUS FOR VALID CHIRALITY REFINEMENT
DO YOU WANT THIS (N) ?
If chirality refinement is requested and there are atoms with the
anomalous dispersion flag turned off, the routine checks that
this is really what you want. This can only appear in
non-centrosymmetric cases when eta is set to refine.
DATA WERE WRITTEN TO XXXXXXX.CD
The program writes all the new data to the .CD file and exits.
80)
** GROUP ** Options
All the questions of this option are not shown, because of the many
paths that might be taken. Appendix 6 contains a more detailed
description of the Rigid Group facility and also an example of a CDEDIT
run using the GROUP option.
(I)
(L)
(G)
(D)
(T)
(M)
(C)
(F)
(Q)
81)
Create IDEALIZED rigid group
LINK idealized rigid groups
GROUP atoms for coupled U or x,y,z parameter refinement
DUAL scattering factors (atoms) on a single site
Link TWO general (non-rigid) atom groups
MAKE new atoms using rigid group definitions
CHECK current groups : LIST/DELETE/(RE)CALCULATE
FINISH calculate groups & return to main menu
QUIT return to main menu without saving run
Q
Q
Q
Q
Q
Q
Q
Q
Set up an Idealized Group (Chemical or Geometric), using data
from the GROUPS.DAT file and atoms from the .CD file.
(See Appendix 6)
81
82
83
84
85
86
87
88
82)
Set up LINKed groups for the LNKREO or LNKRCO group types.
83)
Set up an NATMGP type group
84)
Set up a SCATF2 type group
Page 46
85)
Set up LINKed groups for the LNKGEO or LNKGCO group types.
86)
Generate new atoms from group fragments on the .CD file and group
definitions on the GROUPS.DAT file. In order to do this there
must be at least 3 atoms in the group fragment on the .CD file
in order for the program to successfully fit the whole group.
87)
List, check and edit the current groups on the .GRP file.
88)
Finish the GROUP editting option, write the .GRP file and reorder
the atoms on the .CD file to reflect the current status of the
group specifications.
Page 47
Appendix 5. Explanatory Notes for LSTSQ with BATCH.
$ !
LSBATCH.COM to run LSTSQ as a Batch job
11-Jan-90
$ !
$ ! Any interactive program can be run in batch-mode by making a file
$ ! which contains the instructions to run the program plus the
$ ! interactive responses the program requires. Use the system editor
$ ! to do this. There are also a few preparatory steps. The example
$ ! below illustrates a simple least-squares batch run.
$ !
$ ! Copy the NAMES.ZZ file to the main directory before starting and
$ ! put the full names of the .CD and .RE files, i.e. with
$ ! sub-directories, in this file, e.g.
$ !
[gabe.ls]ruby.cd
$ !
[gabe.ls]ruby.re
$ !
$ ! Force the log to be kept as LSBATCH.LOG in the main directory
$ !
$ ! Run LSTSQ from the appropriate directory
$ !
$ ! Accept the .CD and .RE files on NAMES.ZZ
$ !
$ ! Do 2 cycles of least-squares
$ !
$ ! Dont take defaults and tell the routine it's a batch job with
$ ! option 10. This does NOT appear in the interactive options
$ ! list because it MUST not be selected interactively. The blank
$ ! line is the options terminator
$ !
$ ! Select full-matrix leas-squares
$ !
$ ! No more calculations
$ !
$ define sys$print dummy
$ R [gabe]lstsq
y
y
2
n
10
f
n
$ exit
The Batch-mode is then invoked by submitting this file from the
terminal with
SUBMIT LSBATCH
the job number is reported to the terminal and it can be checked, to see
if it is running, with
SHOW SYS
Page 48
Appendix 6.
Explanatory Notes for LSTSQ with Rigid Groups
It is now possible to refine a variety of constrained systems with
the NRCVAX least-squares routine, LSTSQ. Most of the more useful types
of constraint are available. The facility needs two files in order to
run. Firstly, the file GROUPS.DAT which is a library of idealized group
types must be available. Secondly, a .GRP file is set up with new
commands in CDEDIT, by fitting idealized groups from the GROUPS.DAT file
to specified groups of atoms from the .CD file. The .GRP file contains
the group refinement flags and the group origin (Xg,Yg,Zg) and
orientation angles (Phi,Theta,Rho) for each group to be used. The .GRP
file is read by LSTSQ to determine the constraints to be applied and it
is updated after each cycle of least-squares. It can also be further
editted with CDEDIT.
The .GRP file is an ASCII file and it can be modified with a standard
editor. However, the refinement flags on the .GRP file must match those
on the .CD file and unless the user is very familiar with the internal
.CD file structure it is not advisable to edit the .GRP file in this
way. CDEDIT ensures that all flags on the .GRP and .CD files are set
so that no conflicts are created and is therefore a much safer way to
change the .GRP file. It is also necessary that all group atoms be at
the end of the atom list on the .CD file in consecutive group order and
CDEDIT ensures that this is so. This means that if atoms are added to or
subtracted from the .CD file, the group option of CDEDIT should be run
again to ensure that the .GRP file is correct. It may be a good idea to
make a backup copy of the .CD file before attempting to use groups.
In order for a group of atoms to be treated as an idealized rigid
group there must be an entry in the group library file, GROUPS.DAT,
which describes the group to LSTSQ. This is also an ASCII file and can
be editted, but again in order to make changes it is preferable to use
the program GPADDR in UTILTY which is specifically for this purpose
(see below). The GROUPS.DAT file contains two classes of groups which
are functionally the same.
Firstly, there are common CHEMICAL groups, e.g. phenyl, perchlorate
etc. Atoms in chemical groups are defined in terms of orthogonal
Angstrom coordinates for the lengths and angles of the particular group.
Other such groups can be added to the file quite easily with the routine
GPADDR.
Page 49
Secondly, there are GEOMETRIC groups which describe commonly
occurring geometric shapes (tetrahedra, bipyramids etc) in terms of up
to two bond lengths and an interbond angle which must be supplied by the
user in CDEDIT.
These groups are provided to allow users to define a
rigid group in a flexible way with the minimum number of parameters. For
geometric groups the atoms are described in such a way that the
orthogonal Angstrom coordinates can be generated for the bond-lengths
and angle given in the appropriate record on the .GRP file. The bond
lengths are always specified in the order equatorial then axial,
followed by the inter-bond angle, if needed. Because there are specific
calculations involved for each such group, it is NOT possible to add new
GEOMETRIC groups to the GROUPS.DAT file.
It is ESSENTIAL that the sequence of group atoms from the .CD file be
specified in a SPATIALLY IDENTICAL manner to the sequence for the group
on the GROUPS.DAT file.
Group Refinement Options
-----------------------1. Refinement of Idealized Rigid-groups
This option (and 2. below) uses a library of idealized groups,
CHEMICAL or GEOMETRIC, from the file GROUPS.DAT which are fitted to one
or more atoms on the .CD file, initially by CDEDIT and then by LSTSQ
itself. Parameters are divided into four categories occupancy,
positional, rotational and thermal. Each of these categories, except
rotation, can be refined as group or individual parameters. The
rotation angles can only be refined as group parameters. Occupancy
and/or thermal parameters which are refined as a group can have
DIFFERENT values for different atoms in the group, but the SAME shift
will be applied to all.
When the rigid-group option is selected at least ONE of the four
parameter categories MUST be selected for group refinement and the
refinement flags on the .GRP file MUST agree with those on the .CD file,
though the .GRP flags take precedence over the .CD file individual atom
flags.
It is not possible to refine group positional or rotational
parameters if any of the group atoms are in special positions and CDEDIT
will check for this.
2. Refinement of Two Linked Idealized Rigid-groups (LNKREO, LNKRCO)
This option allows two ideal groups, CHEMICAL or GEOMETRIC, to be
refined so that occupancy, positional and thermal parameters are linked,
but the two sets of rotation parameters can be different. The two group
occupancies can be constrained to be equal (LNKREO, Occ2 = Occ1) or
complementary (LNKRCO, Occ2 = 1 - Occ1). The total occupancy of
corresponding pairs of atoms in the two groups can be specified (default
1.0). In addition it is possible to exclude a specified number of atoms
from the first group from the occupancy refinement. This is useful for
occupancy refinement of disordered groups, where a central atom is
surrounded by two possible orientations of disordered substituents.
Page 50
3. Refinement of a Group of n Atoms (NATMGP)
This option allows parameters of a group of n atoms to be refined as
group values, without imposing the geometric constraints of an ideal
rigid group. Thus the initial geometry is preserved if group positional
parameters are refined and group shifts may be applied to any or all of
the occupancy, positional and thermal parameters of the group. This
could for example, be used to give the same thermal shift to a group of
hydrogen atoms.
4. Refinement of Two Linked Groups of n Atoms (LNKGEO, LNKGCO)
This option allows two groups of n atoms (option 3) to be refined
together, without imposing the geometric constraints of ideal rigid
groups of option 2. This is useful for linking occupancy and thermal
parameters of similar groups, without forcing them to have identical
geometry. The group occupancies can be treated in the same way as
2. above. Thus, a group of atoms disordered over two sites could be
refined as two groups with complementary occupancies.
5. Refinement of Atomic Species (SCATF2)
This option allows the refinement of the proportion of two atomic
species or scattering factors, a and b, on a single site so that
Occb = 1 - Occa, under the constraint that the total site occupancy is
Tot = Frac*(Occa + Occb). Frac is a fixed input value (usually 1.0).
All other parameters are free to vary in the normal way. An example
could be refinement of a mixture of Fe and Mn on one site in a mineral
structure.
Desription of the GROUPS.DAT File
--------------------------------CHEMICAL Groups Available
1.
2.
3.
4.
5.
6.
7.
Phenyl
Phenyl
Perchlorate
Perchlorate
Benzyl
Tolyl
PF6
PHEN01
PHEN02
PERCLO
PEROXY
BZYL01
TOYL01
PF6OH1
C6
C6
Cl O4
O4
C6 H5
C7
P F6
(Dec. 89)
Origin on first atom
Origin at centre of ring
Origin on Cl
Perchlorate oxygens only
p-tolyl. Origin on first ring atom
Octahedral P F6
GEOMETRIC Groups Available
1. Refinement of a Constrained Bond (GCBOND)
This is really a specialized version of a regular idealized rigid
group. The 2 atoms are treated as a group and the bond distance is
constrained to an input value.
2. Refinement of a Constrained angle (GCANGL)
Again this is a specialized ideal rigid group.
The 3 atoms are
constrained so that the two bond distances and then inter-bond angle
are held constant while the whole group is free to move.
Page 51
3. Refinement of a Triangular Planar Group (GCTPL4 or GNTPL3)
An equilateral triangle of atoms, specified by one bond distance
from the centre. GCTPL4 has a central atom in the triangle, whereas
GNTPL3 does not.
4. Refinement of a Square Planar Group (GCSPL5 or GNSPL4)
As 3. but for a square. GCSPL5 has a central atom.
5. Refinement of a Tetrahedral Group (GCTHD5 or GNTHD4)
An ideal regular tetrahedron, with or without a central atom, can be
constrained so that the 4 distances to the centre and regular geometry
are held constant. The 1 axial and 3 equatorial substituents can have
different bond lengths.
6. Refinement of a Tetragonal Pyramidal Group (GCTPY5 or GNTPY6)
As for 5., but with 1 axial and 4 equatorial distances plus an
inter-bond angle.
7. Refinement of a Trigonal Bipyramid (GCTRB6 or GNTRB5)
As for the TPY groups, the geometry of a group of 5 or 6 atoms is
held constant. The axial and equatorial substituents can have different
bond lengths and the interbond angle is 90.0.
8. Refinement of a Tetragonal Bipyramid (GCTEB7 or GNTEB6)
As for the TRB groups, the geometry of the group of 6 or 7 atoms is
held constant. The axial and equatorial substituents can have different
bond lengths.
Adding New CHEMICAL Groups to the GROUPS.DAT File
------------------------------------------------This information is intended to help users understand the contents
of the GROUPS.DAT file and to facilitate the addition of further
CHEMICAL groups. Such groups can be added by editting the ASCII file,
but it is recommended that the program GPADDR be used for this purpose.
GROUP Requirements
1. Unique GROUP name of up to 6 characters
Any characters are allowed though it is helpful to make the
name a meaningful acronym, PHEN01 etc.
The name MUST NOT start with the letter G, because this
identifies the GEOMETRIC groups.
2. Number of Atoms in the Group
Must be greater than 2.
3. Group Origin Information
The group origin can be located on a group atom, in which case
the origin number is the number of the group atom.
Alternatively,
the origin coordinates can be generated in CDEDIT for the .GRP
file, in which case the origin number should be 0.
Page 52
4. Orientation Data
2 vectors defining the X and Y group axes in terms of
group atom numbers.
Atomic positions for the group are supplied as orthogonal
Angstrom x,y,z values so that :-a. the group X axis, can be defined by a pair of group atoms
with identical y and z coordinates.
e.g. 1 and 2 in the PHEN01 example below;
0.0, 0.0, 0.0 and 1.395, 0.0, 0.0
b. a second vector V2 (not collinear with X), can be defined
by a pair of group atoms with identical z coordinates.
e.g. 1 and 5 below, 0.0, 0.0, 0.0 and 0.0, 2.4162, 0.0.
The Y axis is then calculated by crossing X and V2 to give
the group Z axis and then crossing X and Z to give Y.
5. Descriptive Information for the Group
Each group entry should contain records describing the group
and the order of the atoms therein. Up to 60 characters after
a colon (:) on the header record should be used for essential
identification information. This is used for the brief
listing of groups in CDEDIT and so must uniquely identify the
group. Up to ten additional 80-character lines, each starting
with an exclamation mark (!), may contain further details and
should describe the order of the atoms in the group.
6. Orthogonal x,y,z coordinates in Angstroms for each group atom.
**************************************************************
*
*
* If you intend to use the program GPADDR to add groups to *
* GROUPS.DAT and CDEDIT to set up the .GRP file it is not
*
* essential to read the following more detailed information. *
*
*
**************************************************************
Page 53
Examples for Adding Groups to GROUPS.DAT
---------------------------------------Example 1.
Phenyl group, origin on atom 1
PHEN01 6 112140: PHENYL GROUP (C6) C-C 1.395A Origin on atom 1
! The Phenyl group carbon atoms are numbered 1 to 6 around the ring,
! with atom 1 connected to 2, 6 and another atom in the molecule.
0.0
0.0
0.0
1.395
0.0
0.0
2.0925
1.2081
0.0
1.395
2.4162
0.0
0.0
2.4162
0.0
-0.6975
1.2081
0.0
This breaks down as follows :
Record 1
PHEN01 6 112140: PHENYL GROUP (C6) C-C 1.395A Origin on atom 1
FORMAT (1X,A6,2I3,5I1,': ',A60)
Group Name
PHEN01
Number of Atoms in Group
6
Number of the Origin Atom
1
Definition of vectors 1 and 2 12140 (The last 0 must be present)
--- Group X vector 1-->2
--- Group Y vector 1-->4
Essential Group Description : PHENYL GROUP (C6) C-C 1.395A Origin on
atom 1
Records 2 and 3
! The Phenyl group carbon atoms are numbered 1 to 6 around the ring,
! with atom 1 connected to 2, 6 and another atom in the molecule.
FORMAT (1X,'!',A78)
Remainder of group description (Up to 10 lines permitted)
Records 4 to 9
0.0
0.0
0.0
1.395
0.0
0.0
2.0925
1.2081
0.0
1.395
2.4162
0.0
0.0
2.4162
0.0
-0.6975
1.2081
0.0
FORMAT (3F10.4)
Orthogonal Angstrom group coordinates for 6 atoms in this case.
Page 54
Example 2.
Perchlorate oyxgen atoms ; no group atom on origin (on CL)
.
PEROXY 4 001030: PERCHLORATE OXYGENS ONLY (CLO4) CL-O 1.414 A ; ORIGIN
..CL
!The PERCHLORATE OXYGEN-only (PEROXY) group atoms are numbered from 1
to 4.
1.414
0.
0.0
-0.47124 -0.6666 -1.1545
-0.47124
1.3332
0.0
-0.47124 -0.6666
1.1545
This breaks down as follows :
Record 1
PEROXY 4 001030: PERCHLORATE OXYGENS ONLY (CLO4) CL-O 1.414 A ; ORIGIN
..CL
FORMAT (1X,A6,2I3,5I1,': ',A60)
Group Name
PEROXY
Number of Atoms in Group
4
Number of the Origin Atom
0
(i.e. no group atom on origin)
Definition of vectors 1 and 2 01030 (The last 0 must be present)
--- Group X vector 0-->1 (origin to 1)
--- Group Y vector 0-->3 (origin to 3)
Essential Group Description :
PERCHLORATE OXYGENS ONLY (CLO4) CL-O 1.414 A ; ORIGIN
..CL
Record 2
!The PERCHLORATE OXYGEN-only (PEROXY) group atoms are numbered from 1
to 4.
FORMAT (1X,'!',A78)
Remainder of group description (Up to 10 lines permitted)
Records 3 to 6
1.414
0.
0.0
-0.47124 -0.6666 -1.1545
-0.47124
1.3332
0.0
-0.47124 -0.6666
1.1545
FORMAT (3F10.4)
Orthogonal Angstrom group coordinates for 4 atoms in this case.
Page 55
Detailed Description of the .GRP File
------------------------------------Groups and parameters to be refined as group variables are described
by group records in the .GRP file written by CDEDIT. These records
require the group-name, the group-type, no. of atoms, up to 3 refinement
flags and 6 numeric entries, as
Name, Type, Nag, Isoc, Igp, Miss,
Xg, Yg, Zg, Phi, Theta, Rho
where the fields are :-Name = the 4-character name of the group e.g. GP01,
Type = the 6-character group type as on GROUPS.DAT (e.g. PHEN01 or
GCTHD5) or one of the specific group-type codes,
LNKREO, SCATF2 etc.
Nag = the number of atoms in the group.
Note: All group atoms on the .CD file must come AFTER the non-group
atoms and each successive Nag atoms on the .CD file must
correspond to the Nag atoms of the next idealized group on
the GROUPS.DAT file.
The next 3 fields are group refinement flags, which override the
individual atom parameter refinement flags on the .CD file. If
the group refinement flag is turned on (1) then the flags in the
.CD file corresponding to the parameter must also be turned on.
If the group flag is turned off, the individual flags are used.
Isoc = flag for group U/Occ refinement as 10*Uflag + Occflag
Uflag
= 0/1/2 for dont refine/refine iso/refine aniso
Occflag = 0/1
"
"
"
/ "
Occ
Igp = flag for group origin (Xg,Yg,Zg) and orientation angle
(Phi,Theta,Rho) refinement as 10*Angle + origin
Angle flag = 0/1 for dont refine angles/refine angles
Origin flag = 0/1 "
"
"
origin / "
origin
Miss = the number of atoms in the first group which should not be
included in group occupancy refinement for linked groups.
Xg
coords of the group origin from CDEDIT. For some groups
Yg
= the Xg field is used for the total occupancy and for GEOMETRIC
Zg
groups Xg = Deq, Yg = Dax, Zg = angle Alpha (see below).
Phi
Theta = group rotation angles
Rho
Page 56
1. Idealized Rigid Group
The parameters are as described above, except that Miss = 0.
2. Two Linked Idealized Rigid Groups
A header record is required with
Type LNKREO or LNKRCO
Nag
number of atoms in the first group
Frac total occupancy for pairs of corresponding atoms
The 2 group records are as 1. above, except that for the first group
the Miss field specifies the number of atoms whose occupancies are
not linked with those in the second.
e.g. 2 disordered ClO4 groups on the same site, Cl occupancy 1 and
O occupancies Occ and 1 - Occ. Then the two groups are 5 atoms
(1 Cl and 4 O) for the first and 4 atoms (4 O) for the second.
The Cl atom occupancy is not linked to an atom in the second, i.e.
MISS = 1 on the first record.
3. A Rigid-group of Nag Atoms
Type NATMGP this signifies that the group is made up of the next
Nag atoms on the .CD file
Isoc as above
Igp
only xyz may be refined, i.e only 0 or 1.
The remaining values may be omitted.
4. Two Linked Groups of Nag Atoms
Type LNKGEO or LNKGCO
Nag, Isoc, Igp, Miss and Frac are as defined above.
There is only one record for this type of linked group.
5. A Group for Atom Species Refinement
Type SCATF2
Nag
the number of the second atomic species for this site on the
.CD file.
Xg
total site occupancy (FRAC) as 2. above.
The GEOMETRIC groups require normal refinement flags, but the
contents of the Xg, Yg, Zg fields can be any or all of, an equatorial
bond length Deq, an axial bond length Dax and an angle Alpha describing
the group. The group coding always starts with the letters GC or GN. GC
groups have a central atom in the group and the Xg, Yg, Zg coordinates
of the group are the coordinates of the first group atom on the .CD
file. GN groups do not have a central atom and the Xg, Yg, Zg
coordinates are the mean of the group atom coordinates on the .CD file.
1.
2.
3.
4.
5.
Bond Length
Bond Angle
Triangular Plane
Square Plane
Tetrahedron
GCBOND
GCANGL
GNTPL3/GCTPL4
GNSPL4/GCSPL5
GNTHD4/GNTHD5
Xg
Xg
Xg
Xg
Xg
=
=
=
=
=
Deq
Deq, Yg = Dax, Zg = Alpha
Deq
Deq
Deq, Yg = Dax, Zg = Alpha
(109.4712)
6. Tetragonal Pyramid
GNTPY5/GCTPY6
7. Trigonal Bipyramid
GNTRB5/GCTRB6
8. Tetragonal Bipyramid GNTEB5/GCTEB6
Xg = Deq, Yg = Dax, Zg = Alpha
Xg = Deq, Yg = Dax
Xg = Deq, Yg = Dax
Page 57
The following table summarizes the .GRP file requirements.
( # = value needed;
0 = 0 must be entered;
- = may be omitted )
----------------------------------------------------------------------| Description | Name Type | Nag Isoc Igp Miss | Xg,Yg,Zg Angles |
----------------------------------------------------------------------| Ideal Rigid | #
#
| #
#
#
0
|
# # #
# # # |
----------------------------------------------------------------------| Ideal Linked | #
LNKREO | #
0
0
0
| Frac - - - - |
| Rigid. Equal | #
#
| #
#
#
#
|
# # #
# # # |
| Occupancy
| #
#
| #
#
#
0
|
# # #
# # # |
----------------------------------------------------------------------| Ideal Linked | #
LNKRCO | #
0
0
0
| Frac - - - - |
| Rigid Comp. | #
#
| #
#
#
#
|
# # #
# # # |
| Occupancy
| #
#
| #
#
#
0
|
# # #
# # # |
----------------------------------------------------------------------|
N atoms
| #
NATMGP | #
#
#
|
- - - - - |
----------------------------------------------------------------------| Linked Equal | #
LNKGEO | #
#
#
#
| Frac - - - - |
----------------------------------------------------------------------| Linked Comp. | #
LNKGCO | #
#
#
#
| Frac - - - - |
----------------------------------------------------------------------| Scat.Factor | #
SCATF2 | #
Nf2
0
0
| Frac - - - - |
----------------------------------------------------------------------| Bond Length | #
GCBOND | #
#
#
0
| Deq 0 0
# # # |
----------------------------------------------------------------------| Bond Angle
| #
GCANGL | #
#
#
0
| Deq Dax Alp # # # |
----------------------------------------------------------------------| Triang Plane | #
GNTPL3 | #
#
#
0
| Deq 0 0
# # # |
----------------------------------------------------------------------| Triang Plane | #
GCTPL4 | #
#
#
0
| Deq 0 0
# # # |
----------------------------------------------------------------------| Square Plane | #
GNSPL4 | #
#
#
0
| Deq 0 0
# # # |
----------------------------------------------------------------------| Square Plane | #
GCSPL5 | #
#
#
0
| Deq 0 0
# # # |
----------------------------------------------------------------------| Tetrahedron | #
GNTHD4 | #
#
#
0
| Deq Dax Alp # # # |
|
Alp = 109.4712 |
----------------------------------------------------------------------| Tetrahedron | #
GCTHD5 | #
#
#
0
| Deq Dax Alp # # # |
----------------------------------------------------------------------| Tetrag Pyrmd | #
GNTPY5 | #
#
#
0
| Deq Dax Alp # # # |
----------------------------------------------------------------------| Tetrag Pyrmd | #
GCTPY6 | #
#
#
0
| Deq Dax Alp # # # |
----------------------------------------------------------------------| Trig. Bipyr. | #
GNTRB5 | #
#
#
0
| Deq Dax 0
# # # |
----------------------------------------------------------------------| Trig. Bipyr. | #
GCTRB6 | #
#
#
0
| Deq Dax 0
# # # |
----------------------------------------------------------------------| Tetr. Bipyr. | #
GNTEB6 | #
#
#
0
| Deq Dax 0
# # # |
----------------------------------------------------------------------| Tetr. Bipyr. | #
GCTEB7 | #
#
#
0
| Deq Dax 0
# # # |
-----------------------------------------------------------------------
Page 58
Example of a CDEDIT Group Options Run
------------------------------------The following example of a typical Group option run in CDEDIT,
shows how groups are selected with CDEDIT and written to the .GRP file.
** GROUP ** Options
(I)
(L)
(G)
(D)
(T)
(M)
(C)
(F)
(Q)
Create IDEALIZED rigid group
LINK idealized rigid groups
GROUP atoms for coupled U or x,y,z parameter refinement
DUAL scattering factors (atoms) on a single site
Link TWO general (non-rigid) atom groups
MAKE new atoms using rigid group definitions
CHECK current groups : LIST/DELETE/(RE)CALCULATE
FINISH calculate groups & return to main menu
QUIT return to main menu without saving run
GROUP atom edit option (menu) : L
RETAIN previously defined groups (on NI163.GRP) (Y) ? N
Linked idealized groups :
Complementary OCCUPANCIES (Y) ?
Total occupancy of each two atom site (1.0)
Enter number of atoms in the first (largest) group 5
Skip any of the 5 atoms of the first group to align with second (N) Y
Enter the number of skipped atoms (1) :
Want the available GROUPS list ? (Y)
No. Label #atoms
...... Description ......
--- ----- ---------------1 PHEN01
6 PHENYL GROUP (C6) C-C 1.395 A Origin on 1st group atom
2 PHEN02
6 PHENYL GROUP (C6) C-C 1.395 A Origin at centre of RING
3 PERCLO
5 PERCHLORATE (CLO4) CL-O 1.414 A ; ORIGIN ON CL
4 PEROXY
4 PERCHLORATE OXYGENS ONLY (CLO4) CL-O 1.414 A ; ORIGIN
..CL
5 BZYL01
11 PHENYL WITH ALL H (C6H5) C-C 1.395 C-H 1.08 (C6 THEN H5)
6 TOYL01
7 TOLUENE GROUP (C7) C-C 1.395 C-CH3 1.50 A Origin on atom
1
7 PF6OH1
7 PF6 OCTAHEDRAL ALL P-F 1.58 A ; Origin on P
8 GCBOND
2 BOND (special): constrained bond length between two
atoms
9 GCANGL
3 ANGL (special) : 3 ATOMS defined by 2 DISTANCES + 1
ANGLE
10 GNTPL3
3 Regular triangle, no central atom
11 GCTPL4
4 Regular triangle, with central atom
12 GNSPL4
4 Regular square, no central atom
13 GCSPL4
5 Regular square, with central atom
14 GNTHD4
4 Tetrahedron, with no central atom
15 GCTHD5
5 Tetrahedron, with central atom
16
17
18
19
20
21
22
23
0
GNTRB5
5
GCTRB6
6
GNTPY5
5
GCTPY6
6
GNTEB6
6
GCTEB7
7
ACETAT
4
WCO5
11
to quit
Regular trigonal bipyramid, no central atom
Regular trigonal bipyramid, with central atom
Regular Tetragonal Pyramid, no central atom
Regular Tetragonal Pyramid, with central atom
Regular tetragonal bipyramid, no central atom
Regular tetragonal bipyramid, with central atom
ACETATO C-C 1.50, C=O 1.25 ; Central atom on origin.
W(CO)5 W-C 1.7 C-O 1.2 SQ. PYRAMID
Page 59
Enter your choice (0) : 3
Enter an identifying number [1-99] (1)
Are coordinates for the 5 group atoms on the CD file (Y) ?
PERCLO : PERCHLORATE (CLO4) CL-O 1.414 A ; ORIGIN ON CL
The PERCHLORATE group atoms are numbered from the Chlorine
as 1 followed by 4 oxygens in any order.
Please enter atoms in the order 1,2 ... etc
Enter Group using atom number ranges (N - labels) ? Y
Enter up to 10 ranges. End with CR
24 24
25 28
Refine group origin coordinates (Y) ?
Refine group orientation angles (Y) ?
Refine Temperature factor(s) as a group (N) ? Y
Refine Group ISOTROPIC temperature factor (Y) ?
** WARNING : CL3
will be set Isotropic
Do you want to reset the Isotropic factors to one value (N) ? Y
The current U value is 0.365 Enter new U value ( 0.365) : .10
*** Please enter the SECOND linked Rigid group ***
(group temperature , angle & origin options
will be set to first group values)
Want the available GROUPS list ? (Y) N
0
to quit
enter your choice (0) : 4
Enter an identifying number [1-99] (2)
Are coordinates for the 4 group atoms on the CD file (Y) ?
PEROXY : PERCHLORATE OXYGENS ONLY (CLO4) CL-O 1.414 A ; ORIGIN ..CL
The PERCHLORATE OXYGEN-only (PEROXY) group atoms are numbered from 1 to
4.
Please enter atoms in the order 1,2 ... etc
Enter Group using atom number ranges (N - labels) ?
N.B. Separate each atom LABEL with a comma :
e.g. C 1,C3,C7,C9999,C8,UNKNOWN
Group atom labels : O36,O34,O31,O33
Group PEROXY does not have origin definition coded
Get origin coordinates by averaging the group input coordinates (Y) ? N
Does the origin lie on an atom position (Y)
Enter origin atom name : CL3
Do you want to reset the Isotropic factors to one value (N) ? Y
The current U value is 0.266
Enter new U value ( 0.266) : .10
Page 60
** GROUP ** Options
(I)
(L)
(G)
(D)
(T)
(M)
(C)
(F)
(Q)
Create IDEALIZED rigid group
LINK idealized rigid groups
GROUP atoms for coupled U or x,y,z parameter refinement
DUAL scattering factors (atoms) on a single site
Link TWO general (non-rigid) atom groups
MAKE new atoms using rigid group definitions
CHECK current groups : LIST/DELETE/(RE)CALCULATE
FINISH calculate groups & return to main menu
QUIT return to main menu without saving run
GROUP atom edit option (menu) : G
Enter an identifying number [1-99] (3)
How many different atoms in this GROUP ((0 re-enter) ? 3
Enter Group using atom number ranges (N - labels) ? Y
Enter up to 10 ranges. End with CR
35 37
Refine the occupancies with equal shifts (N) ?
Refine coordinates in equal-shift mode (N) ?
Refine U's as an ISOTROPIC group (Y) ?
Do you want to reset the Isotropic factors to one value (N) ? Y
The current U value is 0.065 Enter new U value ( 0.065) :
** GROUP ** Options
(I)
(L)
(G)
(D)
(T)
(M)
(C)
(F)
(Q)
Create IDEALIZED rigid group
LINK idealized rigid groups
GROUP atoms for coupled U or x,y,z parameter refinement
DUAL scattering factors (atoms) on a single site
Link TWO general (non-rigid) atom groups
MAKE new atoms using rigid group definitions
CHECK current groups : LIST/DELETE/(RE)CALCULATE
FINISH calculate groups & return to main menu
QUIT return to main menu without saving run
GROUP atom edit option (menu) : T
Linked ATOM groups :
Complementary OCCUPANCIES (Y) ?
Total occupancy of each two atom site (1.0)
Enter number of atoms in the first (largest) group 1
Enter an identifying number [1-99] (4)
The atom input order is 1,2,3 ... (to 1) of the first group
followed by 1,2 ... ( to 1) of the second
*** Enter 2 atoms in all ***
Enter Group using atom number ranges (N - labels) ?
N.B. Separate each atom LABEL with a comma :
e.g. C 1,C3,C7,C9999,C8,UNKNOWN
Group atom labels : C7A,C7B
Refine coordinates in equal-shift mode (N) ?
Refine Temperature factor(s) as a group (N) ? Y
Page 61
Refine Group ISOTROPIC temperature factor (Y) ?
Do you want to reset the Isotropic factors to one value (N) ?
** GROUP ** Options
(I)
(L)
(G)
(D)
(T)
(M)
(C)
(F)
(Q)
Create IDEALIZED rigid group
LINK idealized rigid groups
GROUP atoms for coupled U or x,y,z parameter refinement
DUAL scattering factors (atoms) on a single site
Link TWO general (non-rigid) atom groups
MAKE new atoms using rigid group definitions
CHECK current groups : LIST/DELETE/(RE)CALCULATE
FINISH calculate groups & return to main menu
QUIT return to main menu without saving run
GROUP atom edit option (menu) : F
GROUP ATOMS must follow NON-GROUP atoms on the .CD file
Do you want the file so arranged ? (Y)
Order of Groups :
1 2 3 4
NEW ORDER OF ATOMS :
1
6
11
16
21
26
31
36
NI1
N3
C4
C11
C18
O24
O35
O13
2
7
12
17
22
27
32
37
CL1
N4
C5
C12
A2
CL3
O36
O14
3
8
13
18
23
28
33
38
CL2
C1
C6
C13
O12
O32
O34
O15
4
9
14
19
24
29
34
39
N1
C2
C8
C16
O22
O38
O31
C7A
5
10
15
20
25
30
35
40
N2
C3
C9
C17
O23
O39
O33
C7B
GROUP Definitions to be written to NI163.GRP
*** LINK Rigid GROUP number
1 Type LNKRCO linking groups
Complementary occupancy with two group total
1.000
1 &
2
GROUP 1 (LR01)
Type PERCLO
U(grp) 0.103
GROUP params refined : Uiso ; Origin X Y Z ; Orientation .
Skipped atoms in first GROUP : CL3
GROUP 2 (LR02)
Type PEROXY
U(grp)
All other options as for the group
1
0.252
LINKed
Atoms_____Numbers____GroupX____GroupY____GroupZ__Occupancy__U(1,1)
O32
O36
28 32
1.4140
0.0000
0.0000
0.4915
0.100
O38
O34
29 33
-0.4712
-0.6666
-1.1545
0.4915
0.100
O39
O31
30 34
-0.4712
1.3332
0.0000
0.4915
0.100
O35
O33
31 35
-0.4712
-0.6666
1.1545
0.4915
0.100
---------------------------------------------------------------------GROUP 3 (GN03) Type NATMGP with the 3 following atoms in the group :
O13
O14
O15
GROUP params refined : Uiso .
INDIVIDUAL params refined (if coded) : Occupancy ; X Y Z .
---------------------------------------------------------------------LINK non-rigid GROUP 4 (LR04) Type LNKGCO with the 2 following atoms
in two groups :
Page 62
LINKed Atoms
Numbers
C7A
C7B
39 40
GROUP params refined : Uiso ; Complem. OCC. .
Complementary occupancy total 1.000
INDIVIDUAL params refined (if coded) : X Y Z.
---------------------------------------------------------------------OK (Y) ?
At the end of the run the file NI163.GRP will contain the following
lines which are basically instructions to LSTSQ for group refinement and
the group atoms will have been moved to the end of the .CD file.
No. of Groups
LINK LNKRCO 5
LR01 PERCLO 5
11.385
LR02 PEROXY 4
67.760
GN03 NATMGP 3
LR04 LNKGCO 1
5 No. of Non-GP Atoms 26 No. of GP atoms 14
00 00 0 1.00000
11 11 1 0.85890 0.36453 0.24890 142.473 -185.578
-
11 11
0
0.85890
-
10 00
11 00
0
1.00000
0.36453
0.24890
156.465
194.148
Page 63
Appendix 7.
Explanatory Notes for ORTEP with NRCVAX
NRCVAX is an interactive system of programs, whereas ORTEP is
oriented towards batch processing. Because ORTEP is extremely flexible,
its instruction set is rather complex and it would not be easy to make
it totally interactive. The basic instruction format has been kept, but
in order to acheive some degree of interactivity the following changes
have been made.
All cell, symmetry and atomic parameters are read from a .CD file.
Terminal input has been made free-format, with input fields seperated by
commas. A new instruction, 1104, has been added which allows a sequence
of ORTEP instructions to be read from a specified file so that they form
a saved sequence inside the program. Another new instruction, 1200, sets
the stereo switch in the program, to allow stereo images to be viewed
directly on the screen from a single set of picture drawing commands.
The 1200 instruction functions as a flip-flop and it need only be given
once in any run, unless mono views are to be drawn. The complementary
pair of instructions 201 and 203, respectively enable and disable the
plotter when it is connected as described under System Implementation.
A small number of the most frequently used PLTMOL-type commands
have been added to make picture manipulation easier. Normal ORTEP
instructions are available at all times. The PLTMOL commands are :-WF
Write File. Fragt die notwendigen ORTEP-Parameter interaktiv
ab und erzeugt ein File mit den entsprechenden ORTEPInstruktionen.
Bei erstmaligem Aufruf immer zuerst ausf&uuml;hren!
RO Rotate the picture about the x,y or z axes.
The PLTMOL definition of axes has been used, i.e. x out of the
screen, y to the right and z upwards. Rotations are clockwise for
a positive angle when viewing from a positive axial direction
and looking towards the origin. The picture ia automatically
redrawn after a rotation.
If normal ORTEP 502 or 503 instructions are used the axial
definition and sense of rotation is as for ORTEP, i.e. x to the
right, y upwards and z out of the screen. The sense of rotation
is opposite to that for the RO command.
MA Magnify the picture preserving the stereo seperation (if stereo).
ZM Zoom the picture changing the stereo seperation.
The picture is automatically redrawn after RO, MA and ZM.
DM Redraw the picture after changes.
P4 Draw the picture on the plotter and return to screen mode.
PT Write the plot file PRINTRX.OUT for subsequent plotting on a
Printronix P300 dot-matrix printer.
CL Clear the screen.
ST Change the sense of the stereo flip-flop switch, then use DM.
RF Read (and save) an ORTEP instruction file (see 1104 above).
Q
Quit the program and return to alpha mode.
A convenient way to manipulate a molecule is to prepare two files of
instructions before running the program. The first should contain all
the instructions necessary to prepare the program for drawing (PREP). The
second should contain just the sequence to draw the picture (DRAW). It is
best to give any 1200(ST) instructions directly from the terminal in
order
to maintain better control.
Page 64
An instruction sequence to draw and manipulate a molecule would then
be as follows :-1. Read the structure data from the .CD file.
2. Read the PREP file with RF (i.e. ,1104).
3. Issue ST (i.e. ,1200) from the terminal, if stereo is wanted.
4. Read the appropriate DRAW file with RF.
5. At this point the DRAW sequence is saved and the picture can be
rotated and redrawn with RO(,502) and DM(,1103) instructions, or
magnified MA or zoomed ZM. P4 and PT can also be given.
6. If it is necessary to switch from mono to stereo, or vice versa,
issue the ST command and resume at 5.
Examples of simple PREP and DRAW files are shown below for a 28 atom
molecule
PREP File
--------,101,155501,28,1,28,1.7
,301,15,11,30,1.5
,401,155501,-2855501
list
,501,155501,155501,165501,155501,156501
,1102
Calculate the bonds
Setup the picture scaling
Put all atoms in the ATOMS
Set up the axes
DRAW File
--------,604,,,,1.54
2,511
,1,28,1,28,4,.8,1.7,.04
,702
2,812
,1,28,1,28,4,.8,1.7,.04
,1102
Scale the drawing to fit
Eliminate overlap
Draw the atoms
Draw the bonds
The picture scale established by the 604 instruction is decreased by a
factor of 0.95 if the stereo option is in use. This is because it is
possible for the image to overflow the boundaries when the 503 rotation,
implicit in stereo drawing, is applied. A DRAW file, such as the one
above will be automatically called twice when stereo is selected, but
the rescaling implied by the 604 is correct in both cases, because it is
applied to the same coordinate data. The stereo image is acheived by the
plotting routines alone.
The files STRUC.CD, STRUC.OR1 and STRUC.OR2, which are on the magtape,
can be used to draw ORTEP pictures as described above. STRUC.CD can also
be used with PLTMOL, PACKER and PLUTO.
To adapt the PT command to other dot-matrix devices, modify the values
of the 3 symbols IPLOT, ZOYPTX and IPY in the routine CPLPPR.FOR, which
is in the .GEN subdirectory. There are notes in the routine explaining
what these symbols are.
Page 65
Appendix 8.
Explanatory Notes for PPLP
This program allows users to index a powder pattern from a trial cell
or a trial set of indexed lines. There are 3 modes of input.
1. All input from the terminal
If this route is chosen, the users should answer the questions the
program asks. It is probably preferable to use the system editor to
prepare an input file for mode 2 or 3 (see below), rather than
trying to type in a whole set of observed data. The quantities
needed are as follows.
a) The radiation wavelength,
b) The assumed Laue group as a number from the following table.
Laue Code
Group
-1
1
4/m
4
m3m
7
-3
10
-3
12
Laue Code
Laue Code
Group
Group
2/m
2
mmm
3
4/mmm
5
m3
6
6/m
8
6/mmm
9
-3m
11 (not R space-groups)
-3m
13 (R space-groups, rhombohedral
axes)
-3
14
-3m
15 (R space-groups, hexagonal axes)
c) If the Laue Group is 2/m then the unique axis must be specified
as 1 for a, 2 for b and 3 for c.
d) 0 or 1 for Qobs or Dobs output.
e) The assumed cell as a,b,c,alpha,beta,gamma. A blank line is
acceptable if some observed lines are indexed.
f) A file name for the Qobs/Dobs output file.
g) Whether the data contains lines from a standard material. If
the answer is Y, then it is assumed that Si isthe standard
material. If not, the cell dimensions of the standard material
must be given.
h) A correction for the specimen being off the rotation axis may
be applied, in which case the off-axis distance should be given
in mms.
i) Observations are entered as a quantity related to theta,
usually a film measurement in mms and a weight which may be 0 in
which case unit weights will be used. If the observation is for
a standard line the h,k,l values must be given.
j) During the indexing 2theta min. and max. will be required and
also any systematic absence conditions.These conditions are
given in the form
A*h + B*k + C*l = D + E*n
for each type of systematic absence. The equation expresses the
condition to be present and each condition is associated with a
code for the type of reflection it is to be applied to. The
reflection types are 1 00l, 2 0k0, 3 h00, 4 0kl, 5 h0l, 6 hk0,
7 hkl, 8 hhl and 9 h-hl. As an example an n-glide condition on
h0l would be 5,1,0,1,0,2.
2. Input from a Measurement File
This mode is very similar to mode 1. The values for a), b), c) and
Page 66
d) are read from the first line of the file. Values for e) (or
zeroes)
are given on the second line and then lines as for i).The other
answers must be supplied via the terminal in response to prompting
questions.
3. Input from a Qobs/Dobs file
Modes 1 and 2 both generate a Qobs/Dobs output file which may be
used for subsequent input. The file may also be prepared with the
editor and its format is identical to the input for mode 2, except
that Qobs or Dobs is given in place of the measurement quantity
and no standard measurements are allowed.
The best way to become familiar with the program is to run it on the
test data given below. This data is for input via mode 1 or 3 and can be
used to create a Qobs/Dobs file for mode 2.
1.54065,3,0,1
5.923,10.44,7.65,90,90,90
Comments only
23.96
(Indices 1,1,0)
28.71
0,2,1
28.99
1,1,1
32.42
0,0,2
35.72
0,2,2
39.73,0,1,1,1
Standard line for Si
40.39
40.58
41.57
42.11
45.65
46.87
47.97
48.61
50.7
51.43
53.22
53.69
54.97
55.11
58.31
59.11
61.51
62.48
64.38
65.36
66.18,0,2,2,0
Standard
67.67
69.49
70.39
71.12
72.89
73.41
74.5
75.51
75.88
Page 67
76.59
78.51,0,3,1,1
80.20
82.43
82.85
85.69
86.37
86.87
87.73
88.68
89.37
89.99
92.67
93.67
96.74,0,4,0,0
100.39
102.87
104.47
106.88,0,3,3,1
123.17,0,4,2,2
Standard
Standard
Standard
Standard
The 2theta min. and max. values are 0 and 110(if all lines are to be
indexed) and there are 2 absence conditions
h0l
l = 2n
5,0,0,1,0,2
hk0 h + k = 2n
6,1,1,0,0,2
Page 68
Appendix 9.
Sample Output Listings for the Ruby Structure
CDFILE -- THE NRCVAX CRYSTAL DATA FILE PROGRAM
TEST OF RUBY
8-DEC-87
Output file
RUBY.CD
Space Group R -3 C
The Space Group is Centric R-Centered Trigonal
3barm 1
Multiplicity of a General Site is 36
The Equivalent Positions are:
x
y-x
y
y
z
1/2+z
-y
x
Date
x-y
z
x-y 1/2+z
Laue Symmetry
y-x
-y
Real Cell Lattice Constants are
a
4.7609(
2)
b
4.7609(
0)
c
Alpha
90.00(
0)
Beta
90.00(
0)
Gamma
Volume
255.109
Reciprocal Cell Lattice Constants are
a*
0.242538
b*
0.242538
c*
0.076946
Alpha*
90.00
Beta*
90.00
Gamma*
60.00
Volume* 0.3920E-02
The equivalent Rhombohedral cell has a =
Radiation is MO
Lambda =
871208
-x
-x
z
1/2+z
12.9962(
120.00(
5.1305 and alpha =
55.29
0.709300
Linear Absorption Coefficient =
12.78cm**(-1)
Calculated density =
3.982
F000 = 299.91 Sigma2 =
1059.64
E000 = 3.071
Epsilon =
The scattering factor data is
AL Delta-f' = 0.056 Delta-f'' = 0.052
A1,B1,A2,B2
=
6.4202
3.0387
1.9002
0.7426
A3,B3,A4,B4,A5 =
1.5936 31.5472
1.9646 85.0887
1.1151
Atomic weight = 26.9815
Mass Abs coef =
5.043 N=
13
Atoms in the unit cell =
12.0
O
6)
0)
Delta-f' = 0.008 Delta-f'' = 0.006
A1,B1,A2,B2
=
3.0485 13.2771
2.2868
5.7011
A3,B3,A4,B4,A5 =
1.5463
0.3239
0.8670 32.9089
0.2508
Atomic weight = 15.9994
Mass Abs coef =
1.147 N=
8
Atoms in the unit cell =
18.0
0.3437
Page 69
DATRD2 -- THE NRCVAX DATA-REDUCTION PROGRAM
Scaling Step of Data Reduction
TEST OF RUBY
8-DEC-87
Cell Constants
a
4.7609
b
Alpha
90.000 Beta
Volume
255.11
4.7609
c
90.000 Gamma
12.9962
120.000
Reciprocal Cell Constants
a*
0.24254
b*
0.24254
c*
Alpha*
90.000 Beta*
90.000 Gamma*
Volume*
0.00392
Wavelength
0.07695
60.000
0.7093
AL
# of Atoms in Cell 12.
Scattering Factor
6.4202
3.0387
1.9002
1.5936
31.5472
1.9646
Dispersion Terms
0.0560
0.0520
O
# of Atoms in Cell 18.
Scattering Factor
3.0485
13.2771
2.2868
1.5463
0.3239
0.8670
Dispersion Terms
0.0080
0.0060
0.7426
85.0887
1.1151
5.7011
32.9089
0.2508
The Intensity File is RUBY.ID
with recordsize 85
The intensities were measured with Profile-analysis
Attenuation Coeffs. are:
Att(0)=
1.00
Att(1)=
1.88
Att(2)=
3.54
Att(3)=
6.66
Att(4)=
12.52
Att(5)= 170.40
The records
20 to 167 are being analyzed
Page 70
Indices
0
0
6
0
Times
Meas
6
26
0
26
RMS Deviation
from
from
Next
Mean
155.3
130.1
192.8
139.5
<Int.> <Sig.>
13433.7
128.8
31356.2
204.6
% Expt. Instab.
Short
Long
Term
Term
-0.501
-0.136
-0.487
-0.495
The CENTRAL line is the mean value of the standards.
The DOTTED lines are +/- 2 Sigmas for all standards.
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Plot of the scale. The interval between the DOTTED lines is 1%.
The standards used are: 1 2
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69
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:
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Page 72
Spherical Absorption Step of Data Reduction
TEST OF RUBY
8-DEC-87
The Crystal Data File is RUBY.CD
With Recordsize 100
This data has already been treated for Absorption
Mu*R = 0.10
The sample Diameter is 152. microns.
Its Linear Absorption Coefficient is
12.78 cm**-1
The Absorption Coefficient in 10 degree steps of 2-theta is:
1.156
1.156
1.156
1.156
1.156
1.155
1.155
1.154
1.126
1.154
1.153
1.153
1.152
1.152
1.152
1.152
1.152
The 2-theta dependent pathlength correction (45 degree steps):
1.48
1.47
1.45
1.44
1.43
The records
1.155
1.152
20 to 167 are now corrected
Reduction Step of the Data Reduction Program
TEST OF RUBY
8-DEC-87
4 sets of intensities have been measured up to 100.00 degrees
The scale of the scaling step is applied.
The blocks 20 to 167 have been grouped
There are
369 reflections within the 2theta range.
The Min. & Max. Transmission Factors are 0.864784 & 0.888166
TEST OF RUBY
8-DEC-87
Reduced Reflection File RUBY.RE
Length 369 Records
Extinction Length for a reflection with a Structure Factor of 1 Electron
is 0.1276E+04 microns
Secondary Extinction according to Zachariasen (1967) is assumed.
The refined Extinction parameter is the Average Pathlength in a Mosaic
block (in microns)
The Direct Beam Polarization is 0.970
The Intensities below 2.5 Counting Statistics Sigmas are considered to
be Unobserved
Valid
Absences
All
Measurements Accepted
1158
235
1393
Measurements Rejected
5
5
10
Measurements Processed
1163
240
1403
Independent Reflections Measured
304
64
368
Independent Reflections not Meas.
0
0
0
Observed Refl. ( 2.5 Sigmas)
296
17
313
Unobserved Reflections
8
47
55
<Delta(I)>/<I>
Page 73
Observed Accepted only
0.009( 1189)
Observed Rejected only
0.098(
10)
Observed Acc+Rej. Meas
0.010( 1199)
0.008( 1129)
0.593(
60)
0.093(
5)
0.956(
5)
0.010( 1134)
0.679(
65)
Unobserved Accepted only
0.888( 204)
Unobserved Rejected only
0.000(
0)
Unobserved Acc+Rej. Meas
0.888( 204)
0.900(
29)
0.886(
175)
0.000(
0)
0.000(
0)
0.900(
29)
0.886(
175)
ObS+Unobs Accepted only
0.009( 1393)
Obs+Unobs Rejected only
0.098(
10)
Obs+Unobs Acc+Rej. Meas
0.010( 1403)
0.008( 1158)
0.681(
235)
0.093(
5)
0.956(
5)
0.010( 1163)
0.730(
240)
Constants written on the CD File:
Maximum Values are :-h k l
8 8 27,
2theta 99.88,
Fobs 414.10
Number of Entries in the RE File 368
Page 74
Normalization Step of the Data Reduction Program
TEST OF RUBY
8-DEC-87
The Reflection File is RUBY.RE
With Recordsize 32
K(S)/S Curve
K(S)
****.****.****.****.****.****.****.****.****.****.****.****.****.****.***
*.****.
-1.0 .
*
*
*
*
*
*
*
*
*
*
-1.5 .
*
*
*
*
*
*
*
*
*
*
*
*
-2.0 .
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
-2.5 .
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
-3.0
.****.****.****.****.****.****.****.****.****.****.****.****.****.****.**
**.****.
0.0
0.3
0.6
0.9
1.2
S
Page 75
Scale of Fobs
0.3360
Overall Temperature factor: B -0.05A**2, U-0.0006A**2
Number of E-values .GT. Emin
66
Experimental
Av.
Av.
Av.
/E/
/E/
/E/
/E*E/
/E*E-1/
/E/
>1,%
>2,%
>3,%
Theoretical Values related to /E/s
Centro
Noncentro
1.054
1.092
0.771
22.826
8.696
0.000
1.000
0.968
0.798
32.000
5.000
0.300
1.000
0.736
0.886
36.800
1.800
0.010
Distribution of E by Sin(theta)
.LE.Sin(theta)
1
#
h
1
2
3
4
5
4
6
1
1
3
0.7654
0.7524
0.7390
0.7250
0.7105
0.6954
0.6796
0.6630
0.6456
0.6271
0.6075
0.5865
0.5639
0.5394
0.5124
0.4822
0.4476
0.4067
0.3553
0.2820
k
l
3
3
3
1
4
10
0
10
24
20
E.GT.3
E
#
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
h
2.72
2.48
2.45
2.41
2.37
23
24
25
26
27
1
2
1
2
5
E.GT.2
E.GT.1
E.LE.1
3
1
1
2
0
1
2
1
2
3
1
0
2
3
1
0
5
2
1
1
4
5
3
4
3
2
3
5
3
2
6
7
5
3
5
3
7
4
6
4
E
1.73
1.73
1.69
1.69
1.69
k
l
E
#
h
k
12
7
17
10
16
14
11
10
17
9
13
11
11
14
9
15
9
15
12
20
l
1
6
2
5
2
6
14
14
6
6
2.09
2.09
2.09
2.08
2.08
45
46
47
48
49
7
1
0
3
6
1
7
4
5
2
6
6
20
16
16
6
7
8
9
10
1
2
2
2
3
6
2
3
2
2
10
24
14
6
4
2.30
2.27
2.25
2.24
2.23
28
29
30
31
32
3
5
2
7
8
3
3
4
0
1
18
14
10
10
4
2.07
2.04
2.04
2.04
2.04
50
51
52
53
54
3
0
5
3
2
0
3
1
1
7
18
18
10
14
10
1.67
1.67
1.66
1.65
1.64
Page 76
11
12
13
14
15
16
17
18
19
20
21
22
6
4
1
3
3
5
1
3
1
4
6
2
2
1
4
5
3
1
5
1
4
1
0
1
4
6
6
4
0
4
14
20
24
24
0
10
2.19
2.19
2.18
2.16
2.15
2.15
2.14
2.14
2.12
2.12
2.11
2.10
33
34
35
36
37
38
39
40
41
42
43
44
3
4
5
2
2
4
1
4
3
3
5
4
0
0
4
1
4
2
2
4
2
2
5
1
0
10
4
4
4
14
20
6
16
10
6
0
1.98
1.90
1.90
1.86
1.86
1.84
1.79
1.79
1.77
1.76
1.75
1.74
Distribution of /E*E/ by Parity Group
eee
eeo
eoe
eoo
oee
oeo
ooe
1.49 0.24 1.79 0.28 1.78 0.27 2.28
#
56
54
46
46
47
45
37
ooo
0.44
37
55
56
57
58
59
60
61
62
63
64
65
66
5
3
0
4
1
5
1
5
2
7
2
2
1
4
5
2
3
0
0
2
0
1
1
7
16
8
4
20
4
14
10
0
14
0
16
4
1.63
1.62
1.61
1.61
1.60
1.59
1.58
1.57
1.56
1.55
1.54
1.53
Page 77
CDEDIT -- THE NRCVAX CELL DATA EDITTING PROGRAM
At# Atom
Type
Anom
Site Mult Prams
Ocpy
x
y
z
u22
u33
u12
u13
U
u11
u23
1 AL
0.00380
AL
Yes
3
2 O
0.00380
O
Yes
2+
12
ZU 1.0000 0.00000 0.00000 0.35227
u22=u11 2u12=u11u13=0
u23=0
18
X U 1.0000 0.30626 0.30626 0.25000
y=x
u22=u11 u23=-u13
LSTSQ -- THE NRCVAX LEAST-SQUARES PROGRAM
TEST OF RUBY
8-DEC-87
Crystal Data File RUBY.CD
File RUBY.RE
Scale Factor
0.33595 Extinction Coefficient
Atomic Parameters
Name
u13
u23
G
Anom
x
y
z
Reflection
0.00E+00
u11
u22
u33
u12
(u values are printed
x100)
AL
YES
O
YES
1.0000
0.00000
0.00000
0.35227
0.380
1.0000
0.30626
0.30626
0.25000
0.380
Agreement Details for Cycle 1
2 Atoms Included,
5 Variables. Full Matrix Method
296 Reflections Included [Out of 304 Total Reflections]
R1 (0.2308E+04/0.8107E+04) 0.2847
R2 (0.4871E+03/0.1843E+04) 0.2643
Inc Unobs Data
0.2847
0.2643
Sqrt Sum[w(Fo-Fc)**2]/(No-Nv) =
28.5545
k for Fo**2 in wt
0.0000
Summary of Parameter Shifts after Cycle
Old
Change
New
Sigma
Scale Factor
Atom
Param
0.33595
-0.05205
0.28390
0.00809
1
C/S
-6.43
Dist
AL
O
G
x
y
z
1.00000
0.00000
0.00000
0.35227
-0.00006
1.00000
0.00000
0.00000
0.35221
U
0.00380
-0.00486
-0.00106
G
x
y
z
1.00000
0.30626
0.30626
0.25000
U
0.00380
-0.00066
-0.00382
1.00000
0.30560
0.30560
0.25000
-0.00002
0.00040 -0.15 -0.001
Net Shift = 0.001 A
0.00097 -5.02
0.00196
-0.33
-0.003
Net Shift = 0.003 A
0.00121 -3.15
Page 78
Agreement Details for Cycle 2
2 Atoms Included,
5 Variables. Full Matrix Method
296 Reflections Included [Out of 304 Total Reflections]
R1 (0.5128E+03/0.6851E+04) 0.0749
R2 (0.1641E+03/0.1843E+04) 0.0890
Inc Unobs Data
0.0749
0.0890
Sqrt Sum[w(Fo-Fc)**2]/(No-Nv) =
9.6199
k for Fo**2 in wt
0.0000
Summary of Parameter Shifts after Cycle
Old
Change
New
Sigma
Scale Factor
Atom
AL
O
0.28390
-0.00306
0.28085
2
C/S
0.00242
-1.26
Param
Dist
G
x
y
z
1.00000
0.00000
0.00000
0.35221
0.00001
1.00000
0.00000
0.00000
0.35222
U
-0.00106
0.00142
0.00036
G
x
y
z
1.00000
0.30560
0.30560
0.25000
U
-0.00002
0.00024
0.00110
1.00000
0.30585
0.30585
0.25000
0.00108
0.00009
0.10
0.000
Net Shift = 0.000 A
0.00022
6.60
0.00046
0.53
0.001
Net Shift = 0.001 A
0.00027
4.00
Agreement Details for Cycle 3
2 Atoms Included,
5 Variables. Full Matrix Method
296 Reflections Included [Out of 304 Total Reflections]
R1 (0.3588E+03/0.6777E+04) 0.0529
R2 (0.1344E+03/0.1843E+04) 0.0729
Inc Unobs Data
0.0529
0.0729
Sqrt Sum[w(Fo-Fc)**2]/(No-Nv) =
7.8787
k for Fo**2 in wt
0.0000
Summary of Parameter Shifts after Cycle
Old
Change
New
Sigma
Scale Factor
Atom
AL
0.28085
0.00016
0.28101
Param
G
x
0.00204
3
C/S
0.08
Dist
1.00000
0.00000
1.00000
0.00000
O
y
z
0.00000
0.35222
0.00000
0.00000
0.35222
U
0.00036
0.00002
0.00038
0.00008
0.04
0.000
Net Shift = 0.000 A
0.00019
0.11
G
x
1.00000
0.30585
-0.00001
1.00000
0.30584
0.00039
-0.02
0.000
Page 79
y
z
0.30585
0.25000
U
0.00108
0.30584
0.25000
0.00001
0.00108
Net Shift = 0.000 A
0.00024
0.03
Agreement Details for Cycle 4
2 Atoms Included,
5 Variables. Full Matrix Method
296 Reflections Included [Out of 304 Total Reflections]
R1 (0.3600E+03/0.6781E+04) 0.0531
R2 (0.1344E+03/0.1843E+04) 0.0729
Inc Unobs Data
0.0531
0.0729
Sqrt Sum[w(Fo-Fc)**2]/(No-Nv) =
7.8775
k for Fo**2 in wt
0.0000
Summary of Parameter Shifts after Cycle
Old
Change
New
Sigma
Scale Factor
Atom
0.28101
0.00001
0.28101
0.00204
4
C/S
0.00
Param
AL
O
Dist
G
x
y
z
1.00000
0.00000
0.00000
0.35222
0.00000
1.00000
0.00000
0.00000
0.35222
U
0.00038
0.00000
0.00038
G
x
y
z
1.00000
0.30584
0.30584
0.25000
U
0.00108
0.00000
0.00000
1.00000
0.30584
0.30584
0.25000
0.00108
0.00008
0.00
0.000
Net Shift = 0.000 A
0.00019
0.00
0.00039
0.00
0.000
Net Shift = 0.000 A
0.00024
0.00
CDEDIT -- THE NRCVAX CELL DATA EDITTING PROGRAM
At# Atom
Type
Anom
Site Mult Prams
Ocpy
x
y
z
u22
u33
u12
u13
U
u11
u23
1 AL
AL
Yes
3
12
ZU 1.0000 0.00000 0.00000 0.35222
0.00038 0.00038 0.00038 0.00019 0.00000
0.00000
u22=u11 2u12=u11u13=0
u23=0
2 O
O
Yes
2+
18
X U 1.0000 0.30584 0.30584 0.25000
0.00108 0.00108 0.00108 0.00054 0.00000
0.00000
y=x
u22=u11 u23=-u13
Page 80
LSTSQ -- THE NRCVAX LEAST-SQUARES PROGRAM
TEST OF RUBY
8-DEC-87
Crystal Data File RUBY.CD
File RUBY.RE
Scale Factor
0.28101 Extinction Coefficient
Atomic Parameters
Name
u13
u23
G
Anom
x
y
z
Reflection
0.00E+00
u11
u22
u33
u12
(u values are printed
x100)
AL
0.000
O
0.000
1.0000
0.000 YES
1.0000
0.000 YES
0.00000
0.00000
0.35222
0.038
0.038
0.038
0.019
0.30584
0.30584
0.25000
0.108
0.108
0.108
0.054
Agreement Details for Cycle 1
2 Atoms Included,
10 Variables. Full Matrix Method
294 Reflections Included [Out of 304 Total Reflections]
R1 (0.3601E+03/0.6781E+04) 0.0531
R2 (0.3948E+03/0.5179E+04) 0.0762
Inc Unobs Data
0.0531
0.0762
Sqrt Sum[w(Fo-Fc)**2]/(No-Nv) =
23.4242
k for Fo**2 in wt
0.0000
Summary of Parameter Shifts after Cycle
Old
Change
New
Sigma
Scale Factor
Extinction
Atom
AL
O
0.28101
-0.03876
0.24225
0.00E+00
4.47E-01
4.47E-01
1
C/S
0.00211 -18.38
3.51E-02
12.73
Param
Dist
G
x
y
z
1.00000
0.00000
0.00000
0.35222
u11
u22
u33
u12
u13
u23
0.00038
0.00038
0.00038
0.00019
0.00000
0.00000
G
x
1.00000
0.30584
-0.00004
0.00249
0.00264
0.00039
1.00000
0.00000
0.00000
0.35218
0.00286
0.00286
0.00302
0.00143
0.00000
0.00000
1.00000
0.30623
0.00007 -0.66 -0.001
Net Shift = 0.001 A
0.00025
9.84
0.00031
8.50
0.00034
1.16
0.002
y
z
0.30584
0.25000
u11
u22
u33
u12
u13
u23
0.00108
0.00108
0.00108
0.00054
0.00000
0.00000
0.30623
0.25000
0.00223
0.00261
0.00104
0.00034
0.00331
0.00331
0.00369
0.00159
0.00034
-0.00034
Net Shift = 0.002 A
0.00038
5.84
0.00046
0.00042
0.00019
5.70
2.47
1.78
Page 81
Agreement Details for Cycle 2
2 Atoms Included,
10 Variables. Full Matrix Method
295 Reflections Included [Out of 304 Total Reflections]
R1 (0.1191E+03/0.6009E+04) 0.0198
R2 (0.1973E+03/0.5179E+04) 0.0381
Inc Unobs Data
0.0198
0.0381
Sqrt Sum[w(Fo-Fc)**2]/(No-Nv) =
11.6850
k for Fo**2 in wt
0.0000
Summary of Parameter Shifts after Cycle
Old
Change
New
Sigma
Scale Factor
Extinction
Atom
AL
O
2
C/S
0.24225
-0.00630
0.23595
0.00099
-6.34
4.47E-01
3.10E-01
7.57E-01
2.44E-02
12.74
Param
Dist
G
x
y
z
1.00000
0.00000
0.00000
0.35218
u11
u22
u33
u12
u13
u23
0.00286
0.00286
0.00302
0.00143
0.00000
0.00000
G
x
y
z
1.00000
0.30623
0.30623
0.25000
u11
u22
u33
u12
u13
u23
0.00331
0.00331
0.00369
0.00159
0.00034
-0.00034
0.00000
0.00021
0.00021
-0.00004
0.00024
0.00023
0.00013
0.00000
1.00000
0.00000
0.00000
0.35218
0.00307
0.00307
0.00322
0.00154
0.00000
0.00000
1.00000
0.30619
0.30619
0.25000
0.00356
0.00356
0.00392
0.00172
0.00034
-0.00034
0.00003 -0.12
0.000
Net Shift = 0.000 A
0.00011
1.91
0.00013
1.54
0.00014
-0.27
0.000
Net Shift = 0.000 A
0.00016
1.51
0.00020
0.00018
0.00008
1.16
0.74
0.01
Agreement Details for Cycle 3
2 Atoms Included,
10 Variables. Full Matrix Method
295 Reflections Included [Out of 304 Total Reflections]
R1 (0.6882E+02/0.5941E+04) 0.0116
R2 (0.1572E+03/0.5179E+04)
Inc Unobs Data
0.0116
0.0304
0.0304
Sqrt Sum[w(Fo-Fc)**2]/(No-Nv) =
0.0000
9.3121
k for Fo**2 in wt
Summary of Parameter Shifts after Cycle
Old
Change
New
Sigma
Scale Factor
0.23595
-0.00088
0.23507
0.00057
3
C/S
-1.54
Page 82
Extinction
Atom
AL
O
7.57E-01
7.42E-02
8.31E-01
1.81E-02
4.10
Param
Dist
G
x
y
z
1.00000
0.00000
0.00000
0.35218
u11
u22
u33
u12
u13
u23
0.00307
0.00307
0.00322
0.00154
0.00000
0.00000
G
x
y
z
1.00000
0.30619
0.30619
0.25000
u11
u22
u33
u12
u13
u23
0.00356
0.00356
0.00392
0.00172
0.00034
-0.00034
0.00000
0.00003
0.00003
0.00000
0.00004
0.00003
0.00002
0.00000
1.00000
0.00000
0.00000
0.35218
0.00310
0.00310
0.00326
0.00155
0.00000
0.00000
1.00000
0.30619
0.30619
0.25000
0.00360
0.00360
0.00395
0.00174
0.00034
-0.00034
0.00001
0.00
0.000
Net Shift = 0.000 A
0.00006
0.55
0.00007
0.47
0.00007
0.02
0.000
Net Shift = 0.000 A
0.00008
0.50
0.00010
0.00009
0.00004
0.31
0.25
-0.02
Page 83
Appendix 10.
Contents of the .CD file
(All variables are 4 bytes; records are 100 variables.)
(F = Floating point; I = Integer)
Record 1
Var.
F/I
1-12
13-24
25-26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54-59
A4
A4
I
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
60-65
66-68
69
70
71
72
F
I
I
F
F
I
Content
Problem title
Job title
Free
Date as YYMMDD
a
Real cell constants
b
c
Cos(Alpha)
Cos(Beta)
Cos(Gamma)
Sin(Alpha)
Sin(Beta)
Sin(Gamma)
Alpha
Beta
Gamma
a*
Reciprocal cell constants
b*
c*
Cos(Alpha*)
Cos(Beta*)
Cos(Gamma*)
Sin(Alpha*)
Sin(Beta*)
Sin(Gamma*)
Alpha*
Beta*
Gamma*
V volume of the unit cell in cubic angstroms
V* = 1/V
Components of the S-matrix for generation of
(Sin(theta)/lambda)**2 = Sq
Sq = h*h*S(1)+k*k*S(2)+l*l*S(3)+h*k*S(4)+
h*l*S(5)+k*l*S(6)
Std. dev. of a,b,c,cos(Alpha,Beta,Gamma)
Max. values of h, k and l (from DATRD2)
Number of reflections in the .RE file
Fo(max)
Sin(theta)/lambda max.
Number of scale factors used (usually 1)
73-80
F
81-83
A
84-86
F
Average values of E for the parity groups
(eee eeo eoe eoo oee oeo ooe ooo)
Directions for maps, in the order down the page,
across the page and then sections.
Start of the 3 map ranges.
Page 84
87-89
90-92
93
94
95
96
97
F
F
I
I
I
F
F
End of the 3 ranges.
Std. dev. of Alpha,Beta,Gamma
No. of valid reflections measured.
No. of unique reflections measured
No. of significant reflections
Sigma level
Sum(delta(I)/sigma(I)) for equivalent sets
Record 2
1-10
11
A1
I
12
I
13
14
I
I
15
I
16
I
17-28
F
29-100
I
Sgsymb
Laue
Space group symbol as in Int. Tab. V. 1
Laue group no.
1,2,3,4
-1, 2/m, mmm, 4/m
5,6,7,8
4/mmm, -3R, -3mR, -3
9,10,11
-3m1, -31m, 6/m
12,13,14
6/mmm, m3, m3m
Latcen Lattice centering flag
1/2/3/4/5/6/7 for P/A/B/C/I/F/R
Icen
0/1 for acentric/centric
Nsym
number of symmetry matrices given below
( Not including centre of symmetry )
Npolnx Polar axis and unique axis flag
0 for no axis unique, origin defined
1 for a-axis unique, origin defined
2 for b-axis unique, origin defined
3 for c-axis unique, origin defined
4 for no axis unique, origin undefined in-x
5 for a-axis unique, origin undefined in-x
8 for no axis unique, origin undefined in-y
10 for b-axis unique, origin undefined in-y
15 for c-axis unique, origin undefined in-x&y
16 for no axis unique, origin undefined in-z
19 for c-axis unique, origin undefined in-z
22 for b-axis unique, origin undefined in-x&z
25 for a-axis unique, origin undefined in-y&z
28 for no axis unique, origin undefined in-xyz
32 for no axis unique, origin undefined in-111
Ncv
Number of lattice centering vectors
( up to 4 max)
Cen
The lattice centering vectors, such as
1/2,0,1/2 or 2/3,1/3,1/3
Rt
Up to 6 Rt matrices as needed
There are 12 values per set in the order
s1 to s9 followed by t1,t2 and t3. The t
values are in 1/12ths of the cell. Then
h' = h*s1 + k*s2 + l*s3
k' = h*s4 + k*s5 + l*s6
l' = h*s7 + k*s8 + l*s9
Phi' = h*t1 + k*t2 l*t3
Where h,k,l are the original values,
And phi' is the phase shift from hkl to h'k'l'.
The equivalent positions are
Page 85
x' = x*s1 + y*s4 + z*s7 + t1
y' = x*s2 + y*s5 + z*s8 + t2
z' = x*s3 + y*s6 + z*s9 + t3
Records 3 & 4
1-96
97-100
I
-
Rt
Free
Up to 8 Rt matrices if needed
Record 5
1-24
25-40
41-56
57-72
73-88
89-100
I
-
Rt
Atomic
Atomic
Atomic
Atomic
Free
Up to 2 Rt
information
information
information
information
matrices
for atom
for atom
for atom
for atom
if needed
type 9 (see Rec.6,Var.10-25)
type 10
type 11
type 12
Record 6
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17-25
F
I
F
F
F
F
F
F
F
A4
F
I
F
F
F
F
F
26-41
42-57
58-73
74-89
90-100
-
Lambda Wavelength used in data collection
Ntyps
Number of scattering factors (up to 12)
Sigma1 F000/Ncv
Sigma2 Sum((scat.facs. at s=0)**2)
Sigma3 Sum((scat.facs. at s=0)**3)
E000
Sigma1/(Sigma2)**(1/2)
Eps
Sigma3/(Sigma2)**(3/2)
Dcal
Density calculated from input data
Abslin Linear absorption coefficient in cm**-1
Atsymb Atomic symbol for atom type #1
Atcnt
No. of this atom type in the unit cell
Iatno
Atomic number
Atwt
Atomic weight
Absco
Mu/Rho
Dfp
Delta-f'
Dfdp
Delta-f"
Sctcof 9 scattering factor coefficients
a1, b1, a2, b2, a3, b3, a4, b4, c such that
f(s) = c + Sigma(ai*exp(-bi*s**2))
where s = sin(theta/lambda)
Values of ai, bi and c are taken from Int. Tab.
Vol. IV, Table 2.2.b.
The same for atom type 2
The same for atom type 3
The same for atom type 4
The same for atom type 5
Free
Record 7
1-16
17-32
33-48
The same for atom type 6
The same for atom type 7
The same for atom type 8
Page 86
49-56
F
57
I
58
59-67
68-70
71-72
73
74
75
76-79
80-100
I
I
F
A
I
I
I
F
-
Atomic radii for atom type 1 - 8
Cn12 radii from Pearson(1972) "The Chemistry and
Physics of Metals and Alloys", Wiley-Interscience
Isym
Used by PLTMOL to generate symmetry related
atoms and molecules.
Link
Used by PLTMOL for the same purpose.
Matrix for such symmetry generation.
Vector for the same.
Name of link atom in PLTMOL list.
0 if matrix above is to apply to all atoms; 1 if not.
Start of reproduced atom range.
End of range.
Atomic radii for atom type 9 - 12
Free
Record 8
1
2
3
4
F
F
F
F
5
I
6
F
7
I
8
9
10
11
12-16
I
F
F
I
F
17-56
F
57
F
Cut off for less-thans (unused)
Wilson plot B
Fo scale, initially from Wilson plot
Extinction coefficient (Average block size in microns)
Extinction is included as
Fc' = k*Fc/(1 + g*Beta*Fc**2)**1/4 where
Fc' is the ectinction corrected Fc
g
is the extinction coefficient
Beta is derived from ABSORP.
(See Larson A.C., Crystallographic Computing,
Munksgaard, Copenhagen, 1970, page 291.)
If ABSORP is not run Beta = Lp-1.
Scale, extinction and chirality (eta) refinement flags
0 refine all 3,
1 no scale,
2 no extinction,
3 no scale or extinction,
4 no eta,
5 no scale or eta,
6 no extinction or eta
7 none
Prec
The weighting scheme modifier such that
wt = 1/(Sig(Fo)**2 + Prec*Fo**2)
Weighting scheme flag
0 counting statistics wts; 1 unit wts
Number of variables in last l.s. run
Sigma(scale)
Sigma(extinction coeff.)
Number of special symmetry relations
Hughes weight coefficients, FB,A1,B1,A2,B2
where wt = A1*Fobs**B1 for Fobs > FB or
wt = A2*Fobs**B2 for Fobs < FB
Special symmetry relations
For an explanation of these relations see below.
Unextinct fraction of the crystal.
If the Rf value is less than 3%, the crystal can be
described as a central core with extinction, surrounded
58
59
60
F
F
F
by a skin as an unextinct fraction. This is a
reasonable model for crystals which have been ground.
RF with significant reflections only
RW with significant reflections only
RF with all reflections
Page 87
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
F
F
I
I
I
I
I
I
I
I
F
F
F
I
F
F
F
F
F
I
I
I
I
I
F
86
87-100
F
-
RW with all reflections
Goodness of fit
No. of reflections included in LSTSQ
No. of total reflections
No. of atoms included
No.of variables included
Minimum electron density in the last map calculated
Maximum
"
"
" "
"
"
"
Type of map (F,D,E or P)
Maximum shift/sigma ratio from the last L.S. cycle
Minimum transmission factor used in DATRD2
Maximum
"
"
"
"
"
D-calc from DISANG
No. of reflns used for diffractometer cell parameters
Minimum 2-theta for cell parameters
Maximum
"
"
"
"
Crystal dimensions (mm)
"
"
"
"
No. of chemical units in the cell
Number of
significant +,+,+ reflections
"
" insignificant +,+,+
"
"
"
significant -,-,"
(Friedel)
"
" insignificant -,-,"
Eta, the chirality parameter for non-centric structures.
The value should refine to +1 or -1 within statistics.
Sigma(Eta)
Free
Records 9 thru N + 8
1-2
3-4
5
6
7-9
10
11-15
16-25
26
27
A4
A4,A2
I
F
F
F
F
F
I
I
Atom name
Site symmetry
Sym. opr. flags(see below for a description)
Occpy
Site occupancy
x, y and z
U or U11
Thermal parameter
U22, U33, U12, U13 and U23
The U values are such that
T = exp(-8Pi**2U(sin(theta/lambda)**2)
(for isotropic)
T = exp-2Pi**2(U11(a*)**2 + ...... +
2(U12a*b* +......))
(for anisotropic)
Sigma(parameters)
Iso
Isotropic/anisotropic U's
0/-1
Scattering factor sequence number
This is the index to which scattering factor
(1 to 12) in each reflection record is to be
used for this atom.
28
I
Iref
Refinement flags
These flags are used to control parameter refinement.
13 bits are set as follows (bit 1 is the LSB)
Page 88
Bit 13
" 12
" 11
-
Do/Dont refine G
Allow/Dont allow x refinement
Do/Dont refine x. If bit 12 is set
no x refinement is allowed ie. x is fixed
" 10 y refinement (as bit 12 for x)
"
9 y refinement (as bit 11 for x)
"
8 z refinement (as bit 12 for x)
"
7 z refinement (as bit 11 for x)
"
6 0/1 Do/dont refine U (or U11)
"
5
"
"
"
U22
"
4
"
"
"
U33
"
3
"
"
"
U12
"
2
"
"
"
U13
"
1
"
"
"
U23
Ibx
Location of spec. rel. data
This code refers to the special relations data
encoded in record 8 variables 17-56. The
special relations for each atom are encoded
by CDEDIT and the location of the applicable
relations is stored in Ibx as
1024Nb + Ne where
Nb = the no. of the 1st relation
Ne = the no. of the last relation for
this atom.
The relations are stored consecutively.
Ianom
Include/dont include anom. dispersion (1/0)
Multiplicity of this atom site
Above data from before the last l.s. cycle
x,y,z variance-covariance terms
These terms are derived from the inverse least
squares matrix. The order is xx, xy, xz, yy, yz, zz.
Nbond
No. of bonds from unimol
Name of 1st bonded atom
Bond distance
Name of 2nd bonded atom
Bond distance
Same for bonded atoms 3 to 8
Free
A4
-
Record N+9
Atom name as blanks
Free
29
I
30
31
32-62
63-68
I
I
69
70-71
72
73-74
75
76-93
94-100
I
A4
F
A4
F
1-2
3-100
F
0/1
0/1
0/1
Site symmetry constraints are determined by detecting the
operations of the group which cause the duplication of the site. Since
we wish to hold this to a relatively small set, we force the atoms in
certain types of sites to lie in particular places in the unit cell;
i.e. atoms on a 4-fold axis in a cubic cell must lie on 4(001) and not on
4(100) or 4(010), and atoms on the cubic 3-fold axis must be on 3(111)
and
not on 3(1-1-1). Thus the code recognizes only 61 of the possible 134
orientationally unique sites. See Int. Tab. (1974) Vol.IV. Section 5.5.,
page 324.
For this purpose we need to recognize only 15 of the 64 possible
Page 89
unique rotation matrices. (There are 39 non-redundant matrices.)
The operations chosen are given in the heading of the table below. a word
containing bits to indicate the matrices which cause the duplication
of the atomic site is generated by the code which determines the site
symmetry. The table gives the matrix flags, any one of which if present
requires the symmetry constraint given in the first column of the table.
Thus we only need do a logical "and" of this bit configuration with
that generated in defining the site symmetry to enable us to define the
constraints upon the atomic site. The table includes the necessary flags
for the positional and anisotropic thermal parameters. The extension of
this table to other properties of the site are obvious. The data word
containing these flags is included in the data written into the atom
record on the crystal data file.
1
1
3
3 1
+ 1
+ -4
+
1
1 2+ m+ 2- m4
2
1
1
m
1
1
1
2
1
1
m
1
1
1
m
1
1 -1
2
Value
octal deci.
Constraint
del-x = 0
del-y = 0
del-z = 0
del-y = del-x
del-y =-del-x
del-z = del-x
1
1
0
0
0
0
0
0
0
1
0
1
1
1
1
0
0
0
1
1
0
0
0
0
0
0
1
1
0
0
0
0
0
0
1
0
0
0
1
0
1
0
0
0
0
1
0
0
0
1
1
0
0
0
1
0
0
0
0
0
1
0
1
0
0
0
0
1
0
0
0
0
0
0
1
0
0
0
1
1
0
0
0
0
1
1
1
0
0
0
54063
54113
12525
22200
01400
20000
22579
22603
5461
9344
768
8192
U22
U33
U12
U12
U13
U13
U23
U23
U23
U23
1
0
0
1
1
0
1
0
0
0
1
1
0
0
0
1
0
0
0
1
1
0
1
0
1
0
1
0
0
0
1
0
1
0
1
0
1
0
0
0
1
0
0
0
0
0
0
0
1
0
1
0
0
0
0
0
0
0
1
0
1
0
0
0
0
0
0
1
0
0
1
0
0
0
0
0
0
1
0
0
0
0
1
0
1
0
0
0
0
0
0
0
1
0
1
0
0
0
0
0
0
0
1
0
0
0
1
0
0
0
0
0
1
0
0
0
1
0
0
0
0
0
0
0
1
0
1
0
0
0
0
0
0
0
1
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
77600
20000
14170
40000
54146
20000
54036
00600
03000
20000
32640
8192
6264
16384
22630
8192
22558
384
1536
8192
Operator =
= U11
= U11
= 0
= U11
= 0
= U12
= 0
= U13
=-U13
= U12
Symmetry relations are of 2 types -a. Fixed parameters eg. x = 0
b. Related parameters eg. y = x
The first type are easily dealt with by not refining (fixing)
the parameter. The second type are dealt with by using special
symmetry relations as follows.
If F = f(x,y) and x and y are functions of another independent
parameter v, then
dF/dv = dF/dx.dx/dv + dF/dy.dy/dv.
If y = nx and x = v, then
dF/dv = dF/dx + n.dF/dy is the required derivative.
The information needed to encode this type of relation is the
number for each parameter and the value of n. This is then packed
as 1000(n + 1) +10N(x) + N(y) into one word. the values of N are
1 for occupancy (G), 2,3,4 for x,y,z, 5 for U (or U11) and 6 to 10
for U22, U33, U12, U13, U23. Up to 40 such relations are allowed.
Page 90
Appendix 11.
Contents of the .RE File.
All variables are 4 bytes ; records are 32 variables.
(F = Floating point; I = Integer)
Var.
F/I
1
2
3
4
5
6
7
8
9
10
11
12
13
14-20
21
22
23
F
I
I
I
F
F
F
F
F
F
F
F
F
F
F
F
I
24-27
28
29
30
31
32
F
F
F
F
F
F
Contents
Beta value for extinction
+h
+k
Miller indices
+l
100*epsilon + E (becomes the f" part of Acalc)
Fo(+h+k+l)
Sqrt(Fo weight for +h+k+l)
Ac(+h+k+l)
Bc(+h+k+l)
Ac(+h+k+l) (Dispersion part only)
Bc(+h+k+l) (Dispersion part only)
Sin(Theta/Lambda)
f(1) scattering factor for atom type 1.
f(2) - f(8) scattering factors for atom types 2-8
Fo(-h-k-l)
Sqrt(Fo weight for -h-k-l)
Obs/Unobs and exclusion flags.
0/1 for +h+k+l obs/unobs
0/2 for -h-k-l obs/unobs
16384 for +h+k+l excluded from LS
32768 for -h-k-l excluded from LS
7
for systematic absence
f(9) - f(12) scattering factors for atom type 9-12
Fo**2(+h+k+l) (may be negative)
Sqrt(Fo**2 weight for +h+k+l)
Fo**2(-h-k-l)
Sqrt(Fo**2 weight for -h-k-l)
f" part of Bcalc