RE: [PyMOL] pair_fit crashes

[DeLano, W. <wa...@su...>]

Hi Jeremy,

If the proteins have significant homology, then you can use the align =
command:

align prot1////ca,prot2

which will perform a sequence alignment of prot1 against prot2, and then =
an optimizing fit using the CA positions.  I'm not sure if the help text =
for align got into 0.82, but the next version will definitely have it.

PyMOL's command length is limit to about 1000 characters, which is =
probably what is causing pair_fit to crash.  However, ideally it should =
complain gracefully instead of crashing, so if you have a sample script =
& input PDB files which cause it to crash, please send them to me as =
attachments.

As far as script options go, you've pointed out a hole which I had =
forgotten about, but Robert's suggestion on defining a function call in =
the script is definitely the way to go for now.

Cheers,
Warren


--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606  FAX:(650)-266-3501=20

-----Original Message-----
From: Jeremy Craven [mailto:c.j...@sh...]
Sent: Thursday, September 26, 2002 2:00 AM
To: pym...@li...
Subject: [PyMOL] pair_fit crashes


I have been trying to write a script to overlay two arbitrary proteins =
via my own alignment and the 'pair_fit' command.=20
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 ?=20
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 ....=20
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=20
The script then executed this string with cmd.do=20
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 ?=20
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.=20
A second little quesion is how do you send command line arguments to a =
pymol python script.=20
If I say=20
PyMOL>   run test1.py abcdef=20
it says=20
Traceback (most recent call last):=20
  File "/usr/lib/python1.5/site-packages/pymol/modules/pymol/parser.py", =
line=20
186, in parse=20
    execfile(args[nest][0],pymol_names,pymol_names)=20
IOError: [Errno 2] No such file or directory=20
whereas test1.py really does exist, and "run test1.py" works fine.=20
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 ...)=20
Cheers=20
Jeremy=20
--=20
*************************************************************************=
********

Dr C. Jeremy Craven
Department of Molecular Biology and Biotechnology
University of Sheffield,=20
Firth Court, Western Bank
S10 2TN Sheffield UK

e-mail: c.j...@sh...
http://www.shef.ac.uk/uni/projects/nmr/CJC/CJC.html

Phone:                       x24323=20
From outside Sheffield:      0114 222 4323
From outside UK:             +44 114 2224323
Fax:                         0114 272 8697

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