[Chimera-users] pipes and planks

[Eric Pettersen]

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

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

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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