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
websites
http://www.bioc.uzh.ch/plueckthun
http://www.bioc.uzh.ch/plueckthun/antibody
http://www.bioc.uzh.ch/plueckthun/nanowelt
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