Measuring the distance between an atom and the protein surface
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 -- *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 *
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
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@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@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
-- *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 *
participants (2)
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Elaine Meng -
Sergio Garay