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@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@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@ca #0
> log info:
> minimum distance from #0:1.B@CA to 1752 atoms, 1 surfaces = 1.4814
>
> measure distance #0:58@ca #0
> minimum distance from #0:58.B@CA to 1752 atoms, 1 surfaces = 1.4484
>
> The second selected atom is clearly deeper inside the protein
>
> Thank you in advance
>
> Sergio