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