<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><DIV>On Nov 9, 2007, at 4:11 PM, Dougherty, Matthew T. wrote:</DIV><BLOCKQUOTE type="cite"><P><FONT size="2">I have about 80 pdb datasets, each corresponding to a single helix.<BR> I know I can do one at a time using the gui.<BR> What is the method for scripting?<BR> <BR> thanks, Matt</FONT></P></BLOCKQUOTE><BR></DIV><DIV>Well, looking at the Apply method in choose.py of the PipesAndPlanks extension, it looks like the code would be something like:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>from PipesAndPlanks.base import displayHelices, initialize, deinitialize</DIV><DIV>from chimera import openModels, Molecule</DIV><DIV>from CGLutil import vrml</DIV><DIV>from chimera.misc import getColorByName</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>red = getColorByName("red")</DIV><DIV>for m in openModels.list(modelTypes=[Molecule]):</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>initialize()</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>wrl = vrml.Transform()</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>helices = displayHelices(mol, red, False, 2.5, False, 2.5)</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>for node in helices:</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>wrl.addChild(node)</DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>openModels.open(vrml.vrml(wrl), type="VRML", sameAs=m, identify="%s - P&P script" % m.name)<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>deinitialize()<BR><DIV><BR class="khtml-block-placeholder"></DIV><DIV>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.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> <SPAN class="Apple-converted-space"> </SPAN></SPAN>Eric Pettersen</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> <SPAN class="Apple-converted-space"> </SPAN></SPAN>UCSF Computer Graphics Lab</FONT></P><P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></BODY></HTML>