Hi,
The last line in your script needs to be something like:
cmd.pair_fit("/" + model + "///30-35/CA", "/template///289-294/CA")
or, more compactly:
cmd.pair_fit("/%s///30-35/CA" % model, "/template///289-294/CA")
this will expand the 'model' variable correctly to whatever it was
set to at the top of the loop.
gilleain torrance
On 15 Sep 2005, at 01:50, Xavier Deupi wrote:
Hi,
I'm trying to write a script to load a series of model peptides and
superimpose them to a template structure.
The part that actually loads the models and superimpose them looks
like this:
for i in range(1,100):
model = 'model.pdb.' + str(i)
cmd.load(model)
cmd.hide("everything", model)
cmd.show("ribbon" , model)
cmd.pair_fit ("/model///30-35/CA", "/template///289-294/CA")
The models are properly loaded (from model.pdb.1 to model.pdb.100)
and displayed; i.e. the variable 'model' is being understood by
pymol. But it seems that it is not recognized by the selection in
the pair_fit command. I get the following error message:
Selector-Error: Misplaced ).
Selector-Error: Malformed selection.
( ( model ) <--
ExecutiveRMS-Error: Atom counts between selection sets don't match
(0 != 6).
... which seems a pretty straightforward error message. I've tried
different 'alternative syntaxes', but I can't get the correct form.
Any help?
Thanks in advance
xavi
--
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)
E-mail: xavier.de...@stanford.edu
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021
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