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Hi Elaine, <br>
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Thanks a lot for this. The models that I am analyzing are separated by distances in the range of 20 to >100 angstroms, for which the contacts command/interfaces becomes rather slow. Sounds like I might need a solution outside the Chimera universe.
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Thanks for your help, <br>
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Best, Matthias<span id="ms-outlook-android-cursor"></span> <br>
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<div id="ms-outlook-mobile-signature">Holen Sie sich <a href="https://aka.ms/AAb9ysg">
Outlook für Android</a></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, September 28, 2021 5:19:17 PM<br>
<b>To:</b> Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Possible to measure the shortest distance between two models?</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Matthias,
<div class="">The "contacts" or "clashes" command gives all-by-all distances (and VDW overlaps) between two sets of atoms. You can write all the info to a file or to a log. It does not automatically only give you the shortest distance, but it sorts the output
so that the shortest is first.</div>
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<div class="">For example (these structures are nonphysically on top of each other, but work for illustrating the commands):</div>
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<div class="">open 1zik</div>
<div class="">open 1gcn</div>
<div class="">contacts #1 restrict #2 distanceOnly 5 log true</div>
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<div class="">...shows in the log all the pairwise distances between the two sets of atoms that are within 5 angstroms, with the shortest distance first.</div>
<div class=""> </div>
<div class="">See measurements:</div>
<div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html</a>></div>
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<div class="">Clashes or contacts command:</div>
<div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html</a>></div>
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<div class="">For scripting, instead of "log" you could use "saveFile" to get an output file for each structure pair. What you get in the Log or file looks like this:</div>
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<div class=""><font face="Courier" class=""><span class="" style="font-style:normal">Ignore distances between atoms separated by 4 bonds or less<br class="">
Detect intra-residue distances: False<br class="">
Detect intra-molecule distances: True<br class="">
<br class="">
3030 distances<br class="">
atom1 atom2 overlap distance<br class="">
1gcn #1/A ARG 18 CZ 1zik #2/A LYS 15 O 4.767 0.233<br class="">
1gcn #1/A LYS 12 O 1zik #2/A VAL 9 CA 4.568 0.432<br class="">
1gcn #1/A ARG 18 CD 1zik #2/A LYS 16 CA 4.540 0.460<br class="">
1gcn #1/A ALA 19 O 1zik #2/B LYS 15 CB 4.449 0.551<br class="">
1gcn #1/A TRP 25 CE3 1zik #2/B GLU 22 CB 4.415 0.585<br class="">
1gcn #1/A SER 8 OG 1zik #2/A LYS 3 CE 4.407 0.593<br class="">
1gcn #1/A PHE 22 CE2 1zik #2/B HIS 18 N 4.392 0.608<br class="">
1gcn #1/A LYS 12 NZ 1zik #2/A LEU 5 CB 4.356 0.644<br class="">
1gcn #1/A LYS 12 CD 1zik #2/A LEU 5 O 4.335 0.665<br class="">
1gcn #1/A GLN 20 CA 1zik #2/B LYS 15 CD 4.309 0.691<br class="">
[... etc. ...]</span></font></div>
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<div class="">I hope this helps,</div>
<div class="">Elaine</div>
<div class="">
<div 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="">
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<blockquote type="cite" class="">On Sep 28, 2021, at 2:15 AM, Vorländer,Matthias Kopano via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
<br class="">
Dear all, <br class="">
I am interested in measuring the shortest distance between two models (PDBs) without a priori knowledge of which atoms will be the closest ones. I am planning to do this for a large number of model pairs, therefore it would be great if this would be scriptable.
Is this possible using ChimeraX?<br class="">
Thanks a lot in advance, <br class="">
Best,<br class="">
Matthias<br class="">
</blockquote>
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