<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>
<body>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Great, that might do the trick! Thanks a lot! :) <span id="ms-outlook-android-cursor">
</span></div>
<div><br>
</div>
<div id="ms-outlook-mobile-signature">Holen Sie sich <a href="https://aka.ms/AAb9ysg">
Outlook für Android</a></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<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 8:42:22 PM<br>
<b>To:</b> Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Possible to measure the shortest distance between two models?</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Chimera (not ChimeraX currently) has a "measure distance" command that gives the shortest distance given two sets of atoms and/or surfaces. However, I don't know whether it would be fast enough for your purposes. Also, Chimera is much
slower in dealing with very large structures than ChimeraX.<br>
<br>
See: <<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance</a>><br>
<br>
Elaine<br>
<br>
<br>
> On Sep 28, 2021, at 11:35 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Elaine, <br>
> <br>
> 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.
<br>
> <br>
> Thanks for your help, <br>
> Best, Matthias <br>
> <br>
> Holen Sie sich Outlook für Android<br>
> From: Elaine Meng <meng@cgl.ucsf.edu><br>
> Sent: Tuesday, September 28, 2021 5:19:17 PM<br>
> To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at><br>
> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
> Subject: Re: [chimerax-users] Possible to measure the shortest distance between two models?<br>
> <br>
> Hi Matthias,<br>
> 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.<br>
> <br>
> For example (these structures are nonphysically on top of each other, but work for illustrating the commands):<br>
> <br>
> open 1zik<br>
> open 1gcn<br>
> contacts #1 restrict #2 distanceOnly 5 log true<br>
> <br>
> ...shows in the log all the pairwise distances between the two sets of atoms that are within 5 angstroms, with the shortest distance first.<br>
> <br>
> See measurements:<br>
> <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html">https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html</a>><br>
> <br>
> Clashes or contacts command:<br>
> <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html</a>><br>
> <br>
> 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:<br>
> <br>
> Ignore distances between atoms separated by 4 bonds or less<br>
> Detect intra-residue distances: False<br>
> Detect intra-molecule distances: True<br>
> <br>
> 3030 distances<br>
> atom1 atom2 overlap distance<br>
> 1gcn #1/A ARG 18 CZ 1zik #2/A LYS 15 O 4.767 0.233<br>
> 1gcn #1/A LYS 12 O 1zik #2/A VAL 9 CA 4.568 0.432<br>
> 1gcn #1/A ARG 18 CD 1zik #2/A LYS 16 CA 4.540 0.460<br>
> 1gcn #1/A ALA 19 O 1zik #2/B LYS 15 CB 4.449 0.551<br>
> 1gcn #1/A TRP 25 CE3 1zik #2/B GLU 22 CB 4.415 0.585<br>
> 1gcn #1/A SER 8 OG 1zik #2/A LYS 3 CE 4.407 0.593<br>
> 1gcn #1/A PHE 22 CE2 1zik #2/B HIS 18 N 4.392 0.608<br>
> 1gcn #1/A LYS 12 NZ 1zik #2/A LEU 5 CB 4.356 0.644<br>
> 1gcn #1/A LYS 12 CD 1zik #2/A LEU 5 O 4.335 0.665<br>
> 1gcn #1/A GLN 20 CA 1zik #2/B LYS 15 CD 4.309 0.691<br>
> [... etc. ...]<br>
> <br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D. <br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
>> On Sep 28, 2021, at 2:15 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
>> <br>
>> Dear all, <br>
>> 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>
>> Thanks a lot in advance, <br>
>> Best,<br>
>> Matthias<br>
> <br>
> _______________________________________________<br>
> ChimeraX-users mailing list<br>
> ChimeraX-users@cgl.ucsf.edu<br>
> Manage subscription:<br>
> <a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br>
<br>
</div>
</span></font></div>
</body>
</html>