[PyMOL] using a variable name within a selection

[Xavier D. <Xav...@st...>]

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: Xav...@st...
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021