[Chimera-users] Atom distances

Elaine Meng meng at cgl.ucsf.edu
Sat Mar 3 09:58:04 PST 2012

Hi Kyle,
Not exactly.  Of course (A) you can measure specific distances, and (B) given one set of atoms you can obtain a list of all other atoms within (or beyond) some cutoff distance of the first set, and (C) given a structure you can find all clashes or contacts within some overlap distance (overlap is the overlap of the VDW radii of the two atoms, where a negative value can be specified to find atoms that are close but not overlapping).  The latter may be most similar to what you wanted, but does not allow excluding the closest contacts (uses only lower bound on overlap, not upper bound).

If you're a coder, it could be done with Python scripting, which is beyond my skill set.  If I were doing it, I would use method (C) including writing out a file, and then manually or with some rudimentary scripting, filter the results file by the distances column.

More details on each of the possibilities mentioned above:

(A) Individual distance measurements. 

(B) List of atoms or residues within or beyond zone.  Select the first set of atoms, then use Select... Zone in the menu to select within or beyond a zone of those.  Then you can write out a list of the current selection contents with Actions... Write List. There is a similar example in this tutorial:

(C) Find Clashes/Contacts. You can find all pairwise interactions meeting your criteria within one set of atoms, or between one set of atoms and another, and then show those with lines and write information including atom names, VDW overlaps, and atom center to atom center distances of the corresponding interactions to the Reply Log or to a file.

The tutorial mentioned above also has an example of using the Find Clashes/Contacts tool. The tool is also implemented as the command "findclash."

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

On Mar 3, 2012, at 2:58 AM, Kyle Morris wrote:

> Hi,
> Is there a way in chimera to search a PDB (or any structure file..) for a particular distance and report back in text or visually between what atoms this occurs, i.e. query whether a structure contains atoms spaced at between 5.5-5.6 Å and which ones?
> Thanks in advance for your help, appreciate it!
> Kyle

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