[chimerax-users] Possible to measure the shortest distance between two models?

Tue Sep 28 11:43:42 PDT 2021

Great, that might do the trick! Thanks a lot! :)

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________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, September 28, 2021 8:42:22 PM
To: Vorländer,Matthias Kopano <matthias.vorlaender at imp.ac.at>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Possible to measure the shortest distance between two models?

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.

See: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance>

Elaine

> On Sep 28, 2021, at 11:35 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi Elaine,
>
> 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.
>
> Thanks for your help,
> Best, Matthias
>
> Holen Sie sich Outlook für Android
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, September 28, 2021 5:19:17 PM
> To: Vorländer,Matthias Kopano <matthias.vorlaender at imp.ac.at>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Possible to measure the shortest distance between two models?
>
> Hi Matthias,
> 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.
>
> For example (these structures are nonphysically on top of each other, but work for illustrating the commands):
>
> open 1zik
> open 1gcn
> contacts #1 restrict #2 distanceOnly 5 log true
>
> ...shows in the log all the pairwise distances between the two sets of atoms that are within 5 angstroms, with the shortest distance first.
>
> See measurements:
> <https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html>
>
> Clashes or contacts command:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
>
> 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:
>
> Ignore distances between atoms separated by 4 bonds or less
> Detect intra-residue distances: False
> Detect intra-molecule distances: True
>
> 3030 distances
>        atom1                 atom2          overlap  distance
> 1gcn #1/A ARG 18 CZ   1zik #2/A LYS 15 O     4.767    0.233
> 1gcn #1/A LYS 12 O    1zik #2/A VAL 9 CA     4.568    0.432
> 1gcn #1/A ARG 18 CD   1zik #2/A LYS 16 CA    4.540    0.460
> 1gcn #1/A ALA 19 O    1zik #2/B LYS 15 CB    4.449    0.551
> 1gcn #1/A TRP 25 CE3  1zik #2/B GLU 22 CB    4.415    0.585
> 1gcn #1/A SER 8 OG    1zik #2/A LYS 3 CE     4.407    0.593
> 1gcn #1/A PHE 22 CE2  1zik #2/B HIS 18 N     4.392    0.608
> 1gcn #1/A LYS 12 NZ   1zik #2/A LEU 5 CB     4.356    0.644
> 1gcn #1/A LYS 12 CD   1zik #2/A LEU 5 O      4.335    0.665
> 1gcn #1/A GLN 20 CA   1zik #2/B LYS 15 CD    4.309    0.691
> [... etc. ...]
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Sep 28, 2021, at 2:15 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Dear all,
>> 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?
>> Thanks a lot in advance,
>> Best,
>> Matthias
>
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