This little document just covers the differences between version 2.4
of BobScript and version 2.6a (February 2003 version).
1) Allocation of memory
For certain arrays, the amount of memory can be allocated at run time.
At the moment the most relevant item is map memory. The command comes
immediately before the 'plot' command and is
allocate map mapsize.i;
where mapsize.i is that amount of memory to allocate for holding maps.
2) Reading of maps is now independent of endian issues. So, for example,
a CCP4 binary map written by an SGI can be directly read by a Linux
machine.
3) The MolScript version 2.x shorthand 'res-atom' has been implemented
in BobScript to ease switching between programs. The syntax is that of
an atom selection, and an example is:
cpk res-atom 45 CB;
which is equivalent to
cpk require in residue 45 and atom CB;
4) When drawing planes through sets of atoms it is possible to give
the planes a thickness and to make the edges of these planes be drawn.
The faces of the plane are coloured by planecolour, the edges by
plane2colour.
set planethickness 0.5;
set planeedges on;
5) Representation of thermal ellipsoids is now possible in BobScript.
I just give here an example file that covers all the syntax options.
Suffice it to say that all normal features are provided.
allocate aniso;
plot
window 20;
read
ani "stnaid.pdb" ;
read no-aniso i "stnaid.pdb" ;
transform all
by rotation -0.04000 -0.86925 0.49276
0.89008 0.19309 0.41288
-0.45404 0.45511 0.76598;
transform all by centre position in residue 307;
transform all by rotation y 50;
set
set
set
set
atomradius atom * 0.6 ;
sticksegments 10;
stickradius 0.075 ;
linewidth 0.7, linecolour white;
colour ball-and-stick cpk
from blue via green to red by b-factor from 0 to 20;
transform all by translation -9 4 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
transform all by translation 6 0 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
set material clarity 0.5;
cpk thermal require in molecule i and in residue 307;
set material opaque;
transform all by translation 6 0 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
set planecolour grey 0.5;
cpk thermal cut require in molecule i and in residue 307;
transform all by translation 6 0 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
set material clarity 0.5;
cpk thermal require in molecule ani and in residue 307;
set material opaque;
transform all by translation -18 -8 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
set planecolour grey 0.5;
cpk thermal cut require in molecule ani and in residue 307;
transform all by translation 6 0 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
cpk thermal planes require in molecule ani and in residue 307;
transform all by translation 6 0 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
cpk thermal axes require in molecule ani and in residue 307;
transform all by translation 6 0 0;
ball-and-stick require in residue 307 and in molecule i;
set probability 50;
cpk thermal principal require in molecule ani and in residue 307;
end_plot
That's the end of the story for now... I'm trying to get around to
getting everything nice and shiny again.
Robert Esnouf (robert@strubi.ox.ac.uk)
Oxford, February 2003