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

[Sergio Garay]

Thanks a lot Elaine! This is exactly what I wanted to measure and it works!

Sergio

On Tue, Dec 18, 2018 at 5:15 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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&~@*
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance
> >
>
> I hope this helps,
> Elaine
> -----
> 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
>
>

-- 








*Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs.
BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 -
Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54
(342) 4575-221 *
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