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Hi Eric,</div>
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It works beautifully now! Thanks for all the help! I'm actually impressed that there isn't something that needs significant modification. I've seen lots of code out there that's not as well formed as what I'm guessing was a quick little script Conrad wrote
for someone. You made my day!</div>
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Regards,</div>
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<br>
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Laura<br>
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<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0; margin-bottom:0">-----</p>
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0; margin-bottom:0">Laura C. Morris</p>
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0; margin-bottom:0">Scientific Computing Professional</p>
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0; margin-bottom:0"><span style="font-size:12pt">Edison & Prestegard Labs</span></p>
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0; margin-bottom:0">Complex Carbohydrate Research Center</p>
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0; margin-bottom:0">706-542-6286 (lab 1075)</p>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Friday, June 4, 2021 2:48 PM<br>
<b>To:</b> Laura Morris <lcmorris@uga.edu><br>
<b>Cc:</b> chimera <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] command line clustering (how to select a subSection?)</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space"><font color="BA0C2F">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]</font><br>
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<div>Hi Laura,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>When Conrad wrote this code he must not have tested this alternate code path, but it almost works. You just need to add "from chimera import selection" right above the "s = selection.OSLSelection(osl)"
line (line 100). When I add that, the script works for me.</div>
<div class=""><br class="">
</div>
<div class="">--Eric<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jun 4, 2021, at 11:22 AM, Laura Morris via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div>
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Hi Eric,</div>
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First of all, thanks for your help so far. If you can take a look at the next problem, I would appreciate it.<span class="x_Apple-converted-space"> </span><br class="">
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I think the string suggestion worked for what I asked, but it appears there's another issue with the script. I realize I'm using code that's > 10 yrs old (and things change) but if you (or someone) know what's not right about this next section this would help
me not have to recode NMRCLUST from scratch (which is tempting, but not preferable). OR, if someone knows where NMRCLUST might be available, I'd be happy to download it.<span class="x_Apple-converted-space"> </span><br class="">
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If I don't change anything in the original script, it runs fine (using all heavy atoms presumably). When I change the value of subSelection (given Eric's example string), it runs through the RMSD portion (I think, I get 250 groups of "Running ksdssp" comments,
like below). Then it appears to get hung up in the function _getAtoms<span class="x_Apple-converted-space"> </span><br class="">
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I am running basically what is referred to in the original (2010) posting, namely:</div>
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chimera --nogui 3c4s.test.pdb cluster.py</div>
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The 3c4s.test.pdb is 250 frames from an AMBER md run (just for testing this). The script cluster.py is the same as the one posed from 2010, with the exception of changing subSelection (to subSelection = "@CA" in this case). My Chimera version is "chimera candidate
version 1.15 (build 42258) 2020-12-18 05:17:29 UTC" (in case that matters at all).<span class="x_Apple-converted-space"> </span><br class="">
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[portion of code from cluster.py referred to by output of running script]<br class="">
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def _getAtoms(m, subSelection):
<div class=""> if not subSelection:</div>
<div class=""> #atoms = m.sortedAtoms()</div>
<div class=""> atoms = m.atoms</div>
<div class=""> else:</div>
<div class=""> osl = '%s%s' % (m.oslIdent(), subSelection)</div>
<div class=""> s = selection.OSLSelection(osl)</div>
<div class=""> wanted = s.vertices(asDict=True)</div>
<div class=""> #atoms = [ a for a in m.sortedAtoms() if a in wanted ]</div>
<div class=""> atoms = [ a for a in m.atoms if a in wanted ]</div>
<div class=""> return atoms</div>
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[end of the output from running script]<br class="">
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Computing secondary structure assignments...
<div class="">Computed secondary structure assignments (see reply log)</div>
<div class="">Model 0.250 (3c4s.test.pdb) has no secondary structure assignments. Running ksdssp.</div>
<div class=""><br class="">
</div>
<div class="">Computing secondary structure assignments...</div>
<div class="">Computed secondary structure assignments (see reply log)</div>
<div class="">Compiling cluster.py...</div>
<div class="">Compiling cluster.py succeeded</div>
<div class="">Executing cluster.py...</div>
<div class="">Computing distance matrix</div>
<div class=""> 0.02: created distance matrix</div>
<div class=""><br class="">
</div>
<div class="">Traceback (most recent call last):</div>
<div class=""> File "/opt/UCSF/Chimera64-1.15rc/share/chimeraInit.py", line 760, in init</div>
<div class=""> chimera.openModels.open(a, prefixableType=1)</div>
<div class=""> File "/opt/UCSF/Chimera64-1.15rc/share/chimera/__init__.py", line 1960, in open</div>
<div class=""> models = func(filename, *args, **kw)</div>
<div class=""> File "/opt/UCSF/Chimera64-1.15rc/share/chimera/__init__.py", line 1330, in _openPython</div>
<div class=""> loadFunc(sandboxName, fileName, f)</div>
<div class=""> File "cluster.py", line 113, in <module></div>
<div class=""> main()</div>
<div class=""> File "cluster.py", line 12, in main</div>
<div class=""> clusterInfo = _cluster(modelList, subSelection)</div>
<div class=""> File "cluster.py", line 23, in _cluster</div>
<div class=""> for m in modelList ]</div>
<div class=""> File "cluster.py", line 100, in _getAtoms</div>
<div class=""> s = selection.OSLSelection(osl)</div>
<div class="">NameError: global name 'selection' is not defined</div>
<div class=""><br class="">
</div>
<div class="">Error while processing cluster.py:</div>
<div class="">NameError: global name 'selection' is not defined</div>
<div class=""><br class="">
</div>
<div class=""> File "cluster.py", line 100, in _getAtoms</div>
<div class=""> s = selection.OSLSelection(osl)</div>
<div class=""><br class="">
</div>
<div class="">See reply log for Python traceback.</div>
<div class=""><br class="">
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Laura<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">-----</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Laura C. Morris</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Scientific Computing Professional</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:12pt">Edison & Prestegard Labs</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px">Complex Carbohydrate Research Center</div>
<div class="" style="margin-top:0px; margin-bottom:0px">706-542-6286 (lab 1075)</div>
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<div id="x_divRplyFwdMsg" dir="ltr" class=""><font class="" style="font-size:11pt" face="Calibri, sans-serif"><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>Friday, June 4, 2021 11:36 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Laura Morris <<a href="mailto:lcmorris@uga.edu" class="">lcmorris@uga.edu</a>><br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="x_Apple-converted-space"> </span><<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [Chimera-users] command line clustering (how to select a subSection?)</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space"><font class="" color="BA0C2F">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]</font><br class="">
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<div class="">Hi Laura,
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>Looking at the code from that mail, the subSelection is just a string with the atom spec you want, but without the model number part. So for carbon alphas it would be "@CA". For
the example you gave it would be ":3-55@CA".</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 Jun 4, 2021, at 8:07 AM, Laura Morris via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div>
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Recently I've been clustering in Chimera but running into memory limitations on my system. I'd like to do the clustering on a computer with more RAM, but I need to be able to do this using only the command line. I found an old post (<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html" id="LPlnk325162" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html</a>)
that includes an example script to do the clustering, but I don't know how to change the subSection to the residues and atoms I want. Here's the portion of relevant code:</div>
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<div class=""><span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">def main():
<div class=""> import chimera</div>
<div class=""> modelList = chimera.openModels.list(modelTypes=[chimera.Molecule])</div>
<div class=""> subSelection = None # Change this to CAs or heavy atoms</div>
<div class=""> clusterInfo = _cluster(modelList, subSelection)</div>
<div class=""> saveReps(clusterInfo, "reps.pdb") # Change file name if needed</div>
<span class=""></span><br class="">
</span></div>
</blockquote>
The "Change this to CAs or heavy atoms" is exactly what I want to do, but I have no idea how to do it. If this were command line in Chimera, I'd use something like "select #0:3-55@CA". I know there's a "runCommand" function that can be included (using "from
chimera import runCommand"). Is this used in some way to set subSelection, and if so, how?<br class="">
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Any help is appreciated.</div>
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Regards,</div>
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<div class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
Laura<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">-----</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Laura C. Morris</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Scientific Computing Professional</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="font-size:12pt">Edison & Prestegard Labs</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px">Complex Carbohydrate Research Center</div>
<div class="" style="margin-top:0px; margin-bottom:0px">706-542-6286 (lab 1075)</div>
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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">Chimera-users
mailing list:<span class="x_x_Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" 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">Chimera-users@cgl.ucsf.edu</a><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">Manage
subscription:<span class="x_x_Apple-converted-space"> </span></span><a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" 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">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div>
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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">Chimera-users
mailing list:<span class="x_Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">Chimera-users@cgl.ucsf.edu</a><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">Manage
subscription:<span class="x_Apple-converted-space"> </span></span><a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div>
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