I have been trying to write a script to overlay two arbitrary proteins
via my own alignment and the 'pair_fit' command.
1) After running into the problem I described below I looked through the
pymol-users mailing list as hard as I could and found a statment that
such arbitrary alignment should be in pymol anyhow from vsn 0.80. I am
using 0.82 but cannot find it. Is it there ?
2) Anyhow, (and assuming that I might want to do alignments my own way
anyhow), I created a script which read in an alignment and created a big
long pair_fit command of the form ....
pair_fit (tbr and resi 187 and name ca),(bs and resi 170 and name ca),
(tbr and resi 192 and name ca),(bs and resi 175 and name ca), .... etc
The script then executed this string with cmd.do
If I restricted this to about 10 atom pairs it worked fine. If I allow
more atoms it crashes the program. On linux it gave segmentation
violation. On irix it gave bus error. On irix it gave another message
that implied that maybe the selections had got truncated. On linux it
got as far as giving a sensible 'ExecutiveRMS' message (including a
value for the rmsd and the number of atoms) and then froze and
eventually core dumped. It therefore seems that the long selection has
been accepted properly, but may it corrupts something else as a side
effect ?
Any ideas anyone ?? I wondered about doing all the selections
invidually into named selections and then create a shorter pair_fit
command, but decided I would ask here first.
A second little quesion is how do you send command line arguments to a
pymol python script.
If I say
PyMOL> run test1.py abcdef
it says
Traceback (most recent call last):
File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py",
line
186, in parse
execfile(args[nest][0],pymol_names,pymol_names)
IOError: [Errno 2] No such file or directory
whereas test1.py really does exist, and "run test1.py" works fine.
Otherwise pymol is a great joy to have discovered in the last month or
so, and a project that I hope I can support (e.g. by contributing
scripts like this one once I can get it to work properly ...)
Cheers
Jeremy
--
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Dr C. Jeremy Craven
Department of Molecular Biology and Biotechnology
University of Sheffield,
Firth Court, Western Bank
S10 2TN Sheffield UK
e-mail: c.j.cra...@shef.ac.uk
http://www.shef.ac.uk/uni/projects/nmr/CJC/CJC.html
Phone: x24323
From outside Sheffield: 0114 222 4323
From outside UK: +44 114 2224323
Fax: 0114 272 8697
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