Yes, this works!
Thank you very much for your help!
Annemarie
> On 01 Apr 2016, at 15:17, David Hall <li...@cowsandmilk.net> wrote:
>
> 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
>> <mailto: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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