<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Julian,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>It would seem that the first thing to do would be to get a list of the poses in order. This gets a list of the currently open models:</div><div class=""><br class=""></div><div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"> </span>import chimera</i></div><div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"> </span>models = chimera.openModels.list()</i></div><div class=""><i class=""><br class=""></i></div><div class=""><span style="font-style: normal;" class="">To extract the poses in order, the crucial information to know is that each model has an </span><i class="">id</i><span style="font-style: normal;" class=""> and </span><i class="">subid</i><span style="font-style: normal;" class=""> attribute, so each pose will have and </span><i class="">id</i><span style="font-style: normal;" class=""> of 1. To get a list of them in order then is:</span></div><div class=""><span style="font-style: normal;" class=""><br class=""></span></div><div class=""><span class="Apple-tab-span" style="font-style: normal; white-space: pre;"> </span><i class="">poses = sorted([m for m in models if <a href="http://m.id" class="">m.id</a> == 1], key=lambda m: m.subid)</i></div><div class=""><br class=""></div><div class=""><span style="font-style: normal;" class="">Then the number of poses is obviously </span><i class="">len(poses)</i><span style="font-style: normal;" class="">. For most of the additional things you mentioned, the easiest thing to do is run the </span>equivalent command, <i class="">e.g.</i><span style="font-style: normal;" class="">:</span></div><div class=""><span style="font-style: normal;" class=""><br class=""></span></div><div class=""><span class="Apple-tab-span" style="font-style: normal; white-space: pre;"> </span><i class="">from chimera import runCommand as run</i></div><div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for pose in poses:</i></div><div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"> </span>run("color red %s" % pose)</i></div><div class=""><i class=""><br class=""></i></div><div class=""><span style="font-style: normal;" class="">This may be all you need. But the </span><i class="">run()</i><span style="font-style: normal;" class=""> call doesn't return any values, so for instance if you need to do different things in the Python code depending on </span><i class="">how many</i><span style="font-style: normal;" class=""> hydrogen bonds a pose forms, then you would have to call the underlying Python routine, which does return values. That particular call is FindHBond.findHBonds(models). I can expand on that if you need that kind of info.</span></div><div class=""><span style="font-style: normal;" class=""><br class=""></span></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 3, 2021, at 5:10 AM, Julian Tirado-Rives <<a href="mailto:julian.tirado-rives@yale.edu" class="">julian.tirado-rives@yale.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Chimera (and ChimeraX) team:<br class=""><br class=""> I need to find some python example or code snippet capable of<br class="">looping over all the molecules in a particular model and do some actions<br class="">separately in each one.<br class=""><br class=""> In our research we use several different docking programs and other<br class="">ways of generating poses of protein-ligand complexes, and using several<br class="">different programs to analyze them gets quite complicated. Instead,<br class="">we've found that the easiest way is to generate from each code, or using<br class="">conversion utilities such as babel, a pdb file of the host and a sdf or<br class="">mol2 file containing all the ligand poses and read them into chimera.<br class="">An excellent program, by the way. We use it all the time.<br class=""><br class=""> I would love to automate the process even further by doing all the<br class="">coloring, rendering, Hydrogen Bond and contact analysis, etc. in Python<br class="">rather than manually. I have been trying to do this, but have not found a way to do the following:<br class=""><br class="">If we have, for instance, the host in model #0, and the ligand poses in model #1 (#1.1, #1.2, ..., #1.N):<br class=""><br class="">- Get from chimera the number of molecules in model #1 (e.g what is N)<br class="">- loop from the first #1.1 to the last #1.N molecule<br class="">- do some cations there (e.g select, color, find HB's, etc)<br class=""><br class=""> I think this should be a problem other people have encountered and<br class="">solved before, but I have not been able to find an example in your<br class="">depository, the mailing lists, or even the book ... I would appreciate<br class="">your input.<br class=""><br class="">Thanks for your help, and for an excellent program!<br class=""><br class=""> - Julian -<br class=""><br class=""><br class="">-- <br class=""><br class=""> -----------------------------------------------------------------<br class=""> | Julian Tirado-Rives | |<br class=""> | Department of Chemistry | Phone: (203)432-3356 |<br class=""> | Yale University | Fax: (203)432-6144 |<br class=""> | P. O. Box 208107 | <a href="mailto:Julian.Tirado-Rives@yale.edu" class="">email: Julian.Tirado-Rives@yale.edu</a> |<br class=""> | New Haven, CT 06520-8107 | |<br class=""> -----------------------------------------------------------------<br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>