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Hi,</div>
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<br>
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Thanks for this suggestion. </div>
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<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
I updated my chimeraX to the latest(nightly) build and i wrote a cxc script to measure SASA of CYS,CSO,CSD,OCS residues . I added the commands into .cxc file and used tom's example ( <span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">open
sasa.cxc foreach *.pdb) </span> to run it inside a folder with a set of 1000 pdb structures . The SASA and defattr file is not getting updated for each pdb file.</div>
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<br>
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A sample of the log is as shown below :</div>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<i>open 7BY4_mm1.pdb<br>
</i></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<i>select :CYS12 atoms, 10 bonds, 2 residues, 1 model selected</i>
<div><i>save CYS.defattr attrName r:area selectedOnly trueSaved attribute 'area' o</i><span style="background-color: rgb(255, 255, 0);"><i>f 0 residues</i></span><i> using match mode: 1-to-1 to CYS.defattr</i></div>
<div><i>select :CSO7 atoms, 6 bonds, 1 residue, 1 model selected</i></div>
<i>save CSO.defattr attrName r:area selectedOnly trueSaved attribute 'area' of 0 residues using match mode: 1-to-1 to CSO.defattr</i><br>
</div>
</blockquote>
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<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
I have attached the output to this email along with the cxc script.</div>
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<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
I look forward to hearing your thoughts regarding fixing this.</div>
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<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
Sincerely appreciate your thoughts and comments,</div>
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<br>
</div>
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best,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
Amith</div>
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<br>
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</blockquote>
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<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Tuesday, July 20, 2021 6:24 PM<br>
<b>To:</b> Rangarajan, Amith <Amith.Rangarajan@ucsf.edu><br>
<b>Cc:</b> ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] python loop with ChimeraX</font>
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Amith, It is also possible to run a ChimeraX command script (.cxc) file once on each PDB file in a directory. open myscript.cxc foreach ~/data/*.cif as described in the docs https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile
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</span><span class="" style="font-size:14px">Hi Amith,</span>
<div class=""><span class="" style="font-size:14px"><br class="">
</span></div>
<div class=""><span class="" style="font-size:14px">It is also possible to run a ChimeraX command script (.cxc) file once on each PDB file in a directory.</span>
<div class=""><span class="" style="font-size:14px"><br class="">
</span></div>
<div class=""><span class="" style="font-size:14px"><b class="" style=""><span class="x_Apple-tab-span" style="white-space:pre"></span>open myscript.cxc foreach ~/data/*.cif</b><br class="">
</span>
<div><span class="" style="font-size:14px"><br class="">
</span></div>
<div><span class="" style="font-size:14px">as described in the docs</span></div>
<div><span class="" style="font-size:14px"><br class="">
</span></div>
<div><span class="" style="font-size:14px"><span class="x_Apple-tab-span" style="white-space:pre"></span><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile" class="">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile</a></span></div>
<div><span class="" style="font-size:14px"><br class="">
</span></div>
<div><span class="" style="font-size:14px">That was added after the ChimeraX 1.2 release so would need the ChimeraX daily build to use it.</span></div>
<div><span class="" style="font-size:14px"><br class="">
</span></div>
<div><span class="" style="font-size:14px"><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</span></div>
<div><br class="">
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 20, 2021, at 5:42 PM, Rangarajan, Amith via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">
<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)">Dear Elaine & Eric</span>
<div class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)">
<br class="">
</div>
<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)">Thanks a lot !. i now have a better sense of how to approach this . I will update this thread soon with the results.</span><br class="">
</div>
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<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)"><br class="">
</span></div>
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<span class="" style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)"><br class="">
</span></div>
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best</div>
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Amith</div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Tuesday, July 20, 2021 3:50 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a>><br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span>Rangarajan, Amith <<a href="mailto:Amith.Rangarajan@ucsf.edu" class="">Amith.Rangarajan@ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [chimerax-users] python loop with ChimeraX</font>
<div class=""> </div>
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To supplement Elaine's answer, looping through a set of data files and applying commands to them is done in a fashion very similar to the way it is done in Chimera, and therefore the documentation for how to do it in Chimera is still pretty useful: <a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">Very
Basic Chimera Programming Primer</a>
<div class=""><br class="">
</div>
<div class="">The differences are:</div>
<div class=""><br class="">
</div>
<div class="">1) ChimeraX is Python 3 whereas Chimera is Python 2. That doesn't actually make any difference to the code shown in the example except for the import statements, which would have to change anyway.</div>
<div class=""><br class="">
</div>
<div class="">2) To run a command, instead of:</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span><i class="">from chimera import runCommand</i></div>
<div class=""><i class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>runCommand("color red")</i></div>
<div class=""><br class="">
</div>
<div class="">it's:</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span><i class="">from chimerax.core.commands import run</i></div>
<div class=""><i class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>run(session, "color red")</i></div>
<div class=""><br class="">
</div>
<div class="">3) To issue status messages, instead of:</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span><i class="">from chimera import replyobj</i></div>
<div class=""><i class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>replyobj.status("Processing file")</i></div>
<div class=""><br class="">
</div>
<div class="">it's just:</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span><i class="">session.logger.status("Processing file")</i></div>
<div class=""><br class="">
</div>
<div class="">
<div class="">--Eric</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 20, 2021, at 11:28 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_x_Apple-interchange-newline">
<div class="">
<div class="">One correction, the saved attribute file should have "defattr" filename extension instead of "txt", so my examples should instead be:<br class="">
<br class="">
save /location/myfile.defattr attrName r:area<br class="">
save /location/myfile.defattr attrName r:area selectedOnly true<br class="">
<br class="">
Sorry about that.<br class="">
Elaine<br class="">
<br class="">
<blockquote type="cite" class="">On Jul 20, 2021, at 11:23 AM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
Hi Amith,<br class="">
Seems like two parts to this question:<br class="">
(A) what are the ChimeraX commands (which could be put into a .cxc file)?<br class="">
(B) how to loop over multiple inputs? ...alluded to by "python loop" in your subject line... .cxc files only contain ChimeraX commands, not python.<br class="">
<br class="">
I don't know python, so somebody else would need to address part B, but I can give some hints on part A. However, depending on the solution to part B, you might instead choose to just make a python script instead of using ChimeraX commands directly. The usual
procedure is to figure out the commands first, often with some trial and error of simply typing them in to the command line.<br class="">
<br class="">
Relevant ChimeraX commands are "measure sasa" to assign residue SASA values as an attribute and then "save" to write the file of attribute values.<span class="x_Apple-converted-space"> </span><br class="">
<br class="">
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa</a>><br class="">
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes</a>><br class="">
<br class="">
I'm guessing you want the SASA of the residues but in the context of the complex, i.e. if they are completely buried in the interface between two proteins even though they would be on the surface of one protein by itself, you would still expect SASA zero. In
that case, you'd want the surface to enclose all the proteins in one blob, and then get the SASA of individual residues, and the command would be something like<br class="">
<br class="">
measure sasa protein setAttribute true<br class="">
save /location/myfile.txt attrName r:area<br class="">
<br class="">
However, if you only want to specify certain residues instead of writing a file for all residues, you would need to use "select" command to select them and then save with the selectedOnly option, e.g. something like<br class="">
<br class="">
select /A:24-53 /B:258<br class="">
save /location/myfile.txt attrName r:area selectedOnly true<br class="">
<br class="">
For part B you may need to embed these in some python script where it keeps closing the previous structure, opening a new structure, and substituting a different name for each save file.<br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<blockquote type="cite" class="">On Jul 20, 2021, at 10:12 AM, Rangarajan, Amith via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
Hi,<br class="">
I am new to chimeraX , i want to loop through a set of biological assemblies measuring SASA of selecting residues and write them to a file. I need some help with starting on this .How to include this into the .cxc script? is there a example somewhere?<br class="">
please share your tips and suggestions,<br class="">
thanks everyone !<br class="">
warm regards,<br class="">
Amith<br class="">
</blockquote>
<br class="">
<br class="">
_______________________________________________<br class="">
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<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">
Manage subscription:<br class="">
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_______________________________________________<br class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">
Manage subscription:<br class="">
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">ChimeraX-users
mailing list</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important"><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></span></div>
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