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

[Sergio Garay]

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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*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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