<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="">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><blockquote type="cite" class=""></blockquote></div><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><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="">-- <br class=""><br class="">Feixia Chu, Ph.D.<br class="">Associate Professor<br class="">Molecular, Cellular & Biomedical Sciences<br class="">University of New Hampshire<br class="">Gregg Hall, Rm436<br class="">35 Colovos Rd<br class="">Durham, NH 03824<br class="">Tel 603 862 2436<br class="">_______________________________________________<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>