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
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 ...)




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.craven@shef.ac.uk

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