I think you can use cmd.do
cmd.do("com /DARPin2//A/37-135/CA, object=com2”)
-David
> On Apr 1, 2016, at 8:48 AM, Honegger Annemarie <honeg...@bioc.uzh.ch> wrote:
>
> Hi!
>
> I am trying to automate some model building tasks
>
> this loop in my pml script works just fine, it generates models in which two
> protein domains are joined by a shared helix
> and highlights backbone steric clashes
>
> python
> for i in range(1, 25):
> cmd.fit('/DARPin2//C/15-22/CA','/helix1//B/%d-%d/CA'%(i, i+7),matchmaker
> = -1)
> cmd.save('model_%d.pdb'%i,'/DARPin1//A/1-160 or /helix1//B/1-%d or
> /DARPin2//C/23-169'%(i+7))
> cmd.color('white','DARPin1')
> cmd.color('paleyellow','/DARPin1//A/37-135')
> cmd.hide('spheres')
> cmd.select('clash','/DARPin1//A/1-157/N+CA+C+A within 2.5 of
> /DARPin2//C/26-169/N+CA+C+N')
> cmd.show('spheres','clash')
> cmd.color('red','clash')
> cmd.ray(2048, 1536)
> cmd.png('model_%dA.png'%i)
> cmd.turn('x', -90)
> cmd.ray(2048, 1536)
> cmd.png('model_%dB.png'%i)
> cmd.turn('x', 90)
> cmd.hide('spheres','clash')
> python end
>
>
> Now, to visualize and quantitate the relative domain orientations in the
> models by a pseudo-torsion angle
> between the centers of gravity of the two domains around the axis of the
> shared helix.
>
> #this needs to be done only once:
>
> run py_scripts/center_of_mass.py
> run py_scripts/anglebetweenhelices.py
>
> ...
>
> com /DARPin1//A/37-135/CA, object=com1
> color black, name PS1
> helix_orientation_hbond /helix1//B/159-193
>
> ...
>
> # this would define the center of gravity of the mobile domain and should be
> within the loop:
>
> com /DARPin2//A/37-135/CA, object=com2
>
> however, since “com” is not a standard pymol command, but added by script
> center_of_mass.py,
> I do not know how to use it from within the loop. If I try to use it
> analogous to normal commands, I get the error message:
>
> Traceback (most recent call last):
> File
> "/Users/ahonegger/Desktop/MacPyMOL1.8.0.2.app/Contents/pymol/modules/pymol/parser.py",
> line 157, in parse
> exec(py_block,self.pymol_names,self.pymol_names)
> File "<string>", line 4, in <module>
> AttributeError: 'module' object has no attribute 'com'
>
> Can somebody please help me?
>
> Thanks
> Annemarie
> _______________________________
>
> Dr. Annemarie Honegger PhD
> Department
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
>
> e-Mail: honeg...@bioc.uzh.ch <mailto:honeg...@bioc.uzh.ch>
>
> websites
> http://www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>
> http://www.bioc.uzh.ch/plueckthun/antibody
> <http://www.bioc.uzh.ch/plueckthun/antibody>
> http://www.bioc.uzh.ch/plueckthun/nanowelt
> <http://www.bioc.uzh.ch/plueckthun/nanowelt>
>
>
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