Other structure programs
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Insight II
Swiss PDB-Viewer
QUANTA/CHARMm and Quanta 2005 for proteins
SYBYL with FUGUE and FlexX for drugs
O or FRODO for x-ray
MolMol for NMR
PovChem, Rasmol, CHARMm
Ranges
Zones
give the residue range: 17
or
19 20
0
but not
17 19 20 0
only P than you can pick a range in the graphic
window
Ranges
PROT
WATER
DRUG
All proteins
All waters
All drugs, ligands, ions
NUC
All nucleic acids
SUG
All sugars
ALL
All residues
HELIX
All helical residues
STRAND
All strand residues (-SHEET takes same ranges)
ION
All ions
OXT
All C-terminal oxygens
<RESNAM>
All residues of a certain type
Start with – (minus sign) to remove things from selection. I.e. TOT –SUG
gives everything except sugars.
Numbering
You can number directly a residue
for example 27 in 3ERA the LYS
(or with O27 if you need the number in brackets)
but if LYS is not in m1 but in m3 you
can number it as S2 27 or as U2 27.
Try the numbering with LISTA
WHAT IF> getmol 1boy
Do you mean: /g/data9/data/pdb/1boy.brk Y/N ? y
Give the set-name (1boy.brk) :
1 10
THR THR
11 20
THR TRP
21 30
LEU GLU
31 40
VAL TYR
41 50
GLY ASP
51 60
THR ASP
61 70
ILE VAL
71 80
ALA ARG
81 90
VAL GLU
91 - 100
LEU TYR
101 - 110
TYR LEU
.....................................
WHAT IF> %shosou
ASN
LYS
TRP
THR
TRP
THR
LYS
VAL
SER
GLU
GLU
THR
SER
GLU
VAL
LYS
GLU
ASP
PHE
THR
ASN
THR
VAL
THR
PRO
GLN
SER
CYS
VAL
SER
GLY
SER
ASN
ALA
ASN
LYS
ILE
LYS
ASP
LYS
TYR
SER
PRO
LEU
ALA
PHE
PRO
SER
CYS
LEU
GLN
PRO
ALA
GLU
GLY
TYR
LYS
VAL
THR
PHE
THR
THR
ALA
GLY
PHE
GLN
ASN
THR
ASN
LYS
TYR
ASP
TYR
GLY
GLU
THR
PRO
LEU
ILE
GLN
SER
THR
GLU
LEU
ASN
PRO
PRO
THR
Content of the SOUP. See the writeup for an explanation.
Molecule
1
2
3
Range
1 (
3)
212 ( 213)
213 ( HOH )
WHAT IF>
Type
Set name
211 ( 213) Protein
212 ( 213) E O2 <211
213 ( HOH ) water
( 110)
SET_1boy.brk
SET_1boy.brk
SET_1boy.brk
Three letter codes for menue
The following three letter codes are associated with entire menus.
ACC
Has to do with ACCessibility
BFT
B-FacTor
BLD
BuiLD (mainly protein)
CHK
CHecK
CHI
Torsion angle
CLU
CLUster of 3D related residues
COL
COLour
DG
Distance Geometry rotamer and loop search
DIG
Digitalization (reconstruction from stereo plots)
FAM
FAMily, range of covalently connected residues
GRA
GRAphics
GRI
GRIn and GRId
GRO
GROmos
H2O
Water
HBO
Hydrogen BOnd (potential hydrogen bonds)
HB2
Hydrogen Bond 2nd version (optimal hydrogen bonds)
HSP
HSsP (multiple sequence alignment files)
HST
Helix, Strand, Turn (in other words: secondary structure)
LAB
LABel (not picked label, but label in MOL-item)
MAP
3D electron density, property or probability distribution MAP
NEU
NEUral net
NMR
Nuclear Magnetic Resonanced
Three-letter codes for options
3 letters:
DEL, INI, ON/OFF, TAB,ROW GRA,SHO
but DG
pairs of options:
GET/MAK, SAV/RES
exceptions:
SIMPLE
DIRECT
Colours
The correspondence between
numbers and colours is:
1 Blue
30 Blue-ish purple
60 Purple
90 Red-ish purple
120 Red
150 Orange
180 Yellow
190 Light brown
220 Soft green
240 Green
270 Funny green
300 White-ish green
330 Light blue
360 Blue
Also you can type:
RED, GREEN, YELLOW,
BLUE,PURPLE, ORANGE, CYAN, MAGENTA.
LAST COLOUR COUNTS