<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Probably the simplest way is to just see if you wound up with multiple models or not (i.e. len(openModels.list(modelTypes=Molecule)) > 1). If you just want to use one model per entry regardless of it being NMR or not, don’t loop over the model list but just use the first model in it, i.e. instead of:<div class=""><br class=""></div><div class="">for mol in openModels.list(modelTypes=[Molecule]):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><i class="">indented</i> analysis code</div><div class=""><br class=""></div><div class="">use:</div><div class=""><br class=""></div><div class="">mol = openModels.list(modelTypes=[Molecule])[0]</div><div class=""><i class="">unindented</i> analysis code</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 19, 2015, at 9:10 PM, Feixia <<a href="mailto:feixia.chu@unh.edu" class="">feixia.chu@unh.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Thank you, Eric! </div><div class="">I am still downloading PDB files through Bio.python. I am just interested in the overall distance distribution of residues, say Lys alpha carbon. NMR entries might end up over-representing due to their multiple models. Thank you for pointing it out. Is there a quick way to distinguish crystal structures from NMR structures?</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Feixia</div><div class=""><br class=""></div><div class="">On Wed, 19 Aug 2015 14:17:35 -0400, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:<br class=""></div><br class=""><blockquote style="margin: 0 0 0.80ex; border-left: #0000FF 2px solid; padding-left: 1ex" class="">Hi Feixia,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You could certainly use Chimera to do that. You need to know some Python. Take a look at the Programmer’s Guide:</div><div class=""><br class=""></div><div class=""><a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html" class="">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html</a></div><div class=""><br class=""></div><div class="">In particular, the “basic primer” discusses how to loop over files in a directory and do things to them one by one.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Here’s some example code for printing the lysine CA-CA distances for a single open file. You could take that and move it into the loop described in the basic primer — customizing it as you wish…</div><div class=""><br class=""></div><div class="">from chimera import openModels, Molecule</div># opening NMR files can produce multiple models, so use a loop...<br class=""><div class="">for mol in openModels.list(modelTypes=[Molecule]):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>lysCas = [a for a in mol.atoms if a.name == “CA” and a.residue.type == “LYS”]</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for i, ca1 in enumerate(lysCas):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for ca2 in lysCas[i+1:]:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>print mol.name, ca1, ca2, ca1.coord().distance(ca2.coord())</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On Aug 18, 2015, at 8:36 AM, Feixia <<a href="mailto:feixia.chu@unh.edu" class="">feixia.chu@unh.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hi there,<br class=""><br class="">I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated.<br class=""><br class="">Best,<br class="">Feixia<br class=""><br class=""> </div></blockquote></div></div></blockquote></div>_______________________________________________<br class="">Chimera-dev mailing list<br class=""><a href="mailto:Chimera-dev@cgl.ucsf.edu" class="">Chimera-dev@cgl.ucsf.edu</a><br class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev<br class=""></div></blockquote></div><br class=""></div></body></html>