<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 Subhrangshu,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You would need to be pretty good with Python to do this. First, you would want to look at this: <a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">Very Basic Chimera Programming Primer</a> to get an idea of how to write a script for Chimera to process many data files.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Second, scripting the MD Movie dialog is almost impossible, so I think you want to use the Ensemble Cluster dialog instead. Your workflow would basically be:</div><div class=""><br class=""></div><div class="">1) Open 100 pdb files.</div><div class="">2) Delete the parts you don't want in the clustering calculation (e.g hydrogens)</div><div class="">3) Bring up a Ensemble Cluster dialog for your files.</div><div class="">4) Save the clustering</div><div class="">5) Close your files and the dialog and repeat as necessary</div><div class=""><br class=""><div>Tips on the above:</div><div><br class=""></div><div>#2: There aren't commands that exactly match what the Movie dialog does. "del solvent" and "del H" will delete solvent and hydrogens. "del ions" will delete all ions, so if there are particular metals you would want to preserver, for instance magnesium, you would have to modify that to "del ions & ~ Mg".</div><div><br class=""></div><div>#3: You are going to need to bring up the dialog using Python code, because you will need a Python reference to the dialog. The code for that is:</div><div><br class=""></div><div>from EnsembleMatch import EnsembleCluster</div><div>d = EnsembleCluster(chimera.openModels.list(), "")</div><div><br class=""></div><div>#4: In order to save the clustering, you are going to have to replicate the code for _SaveClusteringInfo.Apply (which uses the dialog instance) found in EnsembleMatch/base.py, which is in <your Chimera installation>/share (or Chimera.app/Contents/Resources/share on a Mac).</div><div><br class=""></div><div>#5: Close the dialog with d.Quit()</div><div><br class=""></div><div><div>--Eric</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div><br class=""></div><blockquote type="cite" class=""><div class="">On Sep 25, 2020, at 12:40 PM, Subhrangshu Das <<a href="mailto:subhrangshu73das@gmail.com" class="">subhrangshu73das@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class="">Dear sir,<br class=""><br class=""></div>I have 100 pdb files. named as output.1.pdb to output.100.pdb<br class=""></div>what i do manually for clustering is as follows<br class=""><br class=""></div>1. select 100 pdbs -> open in chimera -> golto <b class="">File </b>-> <b class="">save PDB.. </b>-> <b class="">Save Multiple Models as PDB File </b>(renamed as all.pdb)<br class=""></div><div class="">2. open chimera -> goto <b class="">Tools </b>-><b class=""> MD/Ensemble Analysis </b>-><b class=""> MD Movie</b><br class=""></div><div class=""><b class=""></b></div>3. in <b class="">Get Ensemble Info </b>dialogue box set -> <i class="">Trajectory format :</i> <b class="">PDB</b> <br class=""></div> <i class="">PDB frames contained in:</i> <b class="">single file<br class=""></b></div><b class=""> Browse </b>to select File <all.pdb> <br class=""></div> <i class="">Use frames </i><b class="">first </b><i class="">through </i><b class="">last<br class=""><br clear="all" class=""></b><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class=""><div class="">4. on click <b class="">OK,</b> a dialogue box pops out, <b class="">MD Movie: PDB trajectory from all.pdb</b>, in which, goto <b class="">Analysis -> Cluster...<br class=""><br class=""></b>5.. on click<b class=""> Cluster,</b> a dialogue box pops out,<b class=""> Get Clustering Parameters,</b> in which I set <i class="">Cluster trajectory </i>as:<br class=""></div><div class=""><i class="">Starting frame: </i><b class="">1<br class=""></b></div><div class=""><i class="">step size: </i><b class="">1</b><i class=""><br class=""></i></div><div class=""><i class="">Ending frame:</i><b class=""> 100<br class=""></b></div><div class=""><i class="">Cluster based on current selection, if any: </i><b class="">true<br class=""></b></div><div class=""><i class="">Ignore solvent and non metal ions: <b class="">true<br class=""></b></i></div><div class=""><i class="">Ignore hydrogens: </i><b class="">true<br class=""></b></div><div class=""><i class="">Ignore metal ions: </i><b class="">alkali<br class=""></b><br class=""></div><div class="">6. on click <b class="">OK, </b>after some RMSD calculation, i get the <b class="">Clustering</b> result, which I save to a text file <cluster> <br class=""></div><div class=""><b class=""><br class=""></b></div><div class="">Now, as I need to do this for multiple times, I want to automate these steps by a python script. Can you please help with a scipt or some command help for the aforesaid tasks. Any help will be helpful in these regard.<br class=""></div><div class=""><b class=""><br class=""><br class=""><br class=""></b></div><div class="">-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Thanks & Regards,<div class=""><br class=""></div><div class="">Subhrangshu Das</div><div class="">Junior Research Fellow, CSIR-IICB<br class=""></div><div class="">Department of Structural Biology & Bioinformatics<br class=""></div><div class="">Contact - IICB TRUE Campus, CN-6, Salt lake, Sector V, Kolkata-700091<span style="font-size:12.8px;background-color:rgb(243,243,243)" class=""><br class=""></span><span style="background-color:rgb(255,255,255)" class=""><span style="font-size:12.8px" class=""><font color="#0000ff" class=""><u class="">+919804938813</u></font><b class=""><font class=""> </font></b></span><span style="color:rgb(0,0,255);font-size:12.8px" class=""></span></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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