[Chimera-users] pipes and planks

Eric Pettersen pett at cgl.ucsf.edu
Fri Nov 9 16:39:47 PST 2007

On Nov 9, 2007, at 4:11 PM, Dougherty, Matthew T. wrote:
> I have about 80 pdb datasets, each corresponding to a single helix.
> I know I can do one at a time using the gui.
> What is the method for scripting?
> thanks, Matt

Well, looking at the Apply method in choose.py of the PipesAndPlanks  
extension, it looks like the code would be something like:

from PipesAndPlanks.base import displayHelices, initialize, deinitialize
from chimera import openModels, Molecule
from CGLutil import vrml
from chimera.misc import getColorByName

red = getColorByName("red")
for m in openModels.list(modelTypes=[Molecule]):
	wrl = vrml.Transform()
	helices = displayHelices(mol, red, False, 2.5, False, 2.5)
	for node in helices:
	openModels.open(vrml.vrml(wrl), type="VRML", sameAs=m, identify="%s  
- P&P script" % m.name)

If haven't tested the above, so it may take a few swift kicks to get  
it to start up and run.  Alternatively, I have been working on an  
extension to measure helix axes that can give you a helix-only  
display like Pipes and Plank and can do multiple models at once.  I  
could send it to you if you want to try it out.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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