[Chimera-users] Does anyone know how to specify a "MarkerSet Link" to be used for findClash

Elaine Meng meng at cgl.ucsf.edu
Sat Jul 8 16:47:08 PDT 2017

Hi Jun Ha Song,
Yes, links are just like bonds, and exist just in terms of connecting those endpoints, so you have to fill them in with atoms/markers for findclash to use.

Q1: sorry, there is no way to specify just bonds in the command line, and even if you did, they wouldn’t be the XYZ-points needed by computations like findclash.  There is “bondzone” to make various zoning tools use points along bonds, but as far as I know it doesn’t affect distance measurements.  You could try it to make sure:

Q2: there is “distance” to report just the distance between two specified atoms/markers and “measure distance” to find just the closest distance between 2 sets of atoms and/or surface vertices… are either of those useful in your case?

For command-line specification, you can use model number and/or residue number (which is apparently the marker ID). When I create a marker file (attached below, test.cmm) from the example given in the Volume Tracer manpage,
… one marker is residue 1 and the other is residue 2, but they don’t appear to have atom names.  So if the marker set is #0, I can use 
sel #0:1
sel #0:2
distance #0:1,2

I don’t know how Tom’s script adds the markers along links (whether they’re in the same model as the original marker set, what residue numbers, etc.)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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> On Jul 8, 2017, at 2:41 PM, Jun Ha Song <junhasong at berkeley.edu> wrote:
> Hello,
> I want to search whether my models are close enough to be exactly apart from each other by the distance I specify.
> findClash appear to be tailor-made for the exact task I was hoping to do, but unfortunately, it appear to only search nearby atoms, not the links, even if I select the entire model which has both markers and links incorporated as its component.
> The only way that I can make my entire MarkerSet to be competent for findClash was to use Tom's dividelinks.py script (http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/dividelinks.py) to add n number of marker s along the link of two marker that I selected.
> Q1. Can I ever specify MarkerSet Link by atom-spec commands, to use findClash on the inter-model links as well, not only for the markers?
> Q2. Is there any other function than findClash that allow me to find any inter-model (never atoms within the same model) atom or link's distance that I specify exist?
> Best,
> Jun Ha Song.

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