[Chimera-users] Measuring the distance between an atom and the protein surface

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 18 12:15:40 PST 2018

Dear Sergio,
I believe you are actually getting the distance from that atom to the nearest other atom.  In other words, “#0” includes all the atoms as well as the surface.

Try something like this where the second spec is model 0 but not its atoms (i.e. surface only):

measure dist #0:5.a at ca #0&~@*


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

> On Dec 18, 2018, at 12:06 PM, Sergio Garay <sergio.alberto.garay at gmail.com> wrote:
> Dear Chimera Users
> I want to measure the distance between an atom (or group of atoms) and the protein surface. I need a sort of residue depth, so the shortest distance between an atom and the molecular surface would be fine for me. I found that command "measure distance" could help, but it does not appear to be working, because every atom that I choose give aproximately the same value. For example (I have only one molecule loaded in Chimera) :.
> measure distance #0:1 at ca #0
> log info:
> minimum distance from #0:1.B at CA to 1752 atoms, 1 surfaces = 1.4814
> measure distance #0:58 at ca #0
> minimum distance from #0:58.B at CA to 1752 atoms, 1 surfaces = 1.4484
> The second selected atom is clearly deeper inside the protein
> Thank you in advance
> Sergio

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