<div dir="ltr"><div class="gmail_default" style="font-size:small">Thanks a lot Elaine! This is exactly what I wanted to measure and it works! <br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Sergio</div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Dec 18, 2018 at 5:15 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Sergio,<br>
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.<br>
<br>
Try something like this where the second spec is model 0 but not its atoms (i.e. surface only):<br>
<br>
measure dist #0:5.a@ca #0&~@*<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Dec 18, 2018, at 12:06 PM, Sergio Garay <<a href="mailto:sergio.alberto.garay@gmail.com" target="_blank">sergio.alberto.garay@gmail.com</a>> wrote:<br>
> <br>
> Dear Chimera Users<br>
> <br>
> 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) :.<br>
> <br>
> measure distance #0:1@ca #0<br>
> log info:<br>
> minimum distance from #0:1.B@CA to 1752 atoms, 1 surfaces = 1.4814<br>
> <br>
> measure distance #0:58@ca #0<br>
> minimum distance from #0:58.B@CA to 1752 atoms, 1 surfaces = 1.4484<br>
> <br>
> The second selected atom is clearly deeper inside the protein<br>
> <br>
> Thank you in advance<br>
> <br>
> Sergio<br>
<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><font color="#0000ff" size="1"><i>Sergio Garay<br>Dr. en Ciencias Biológicas<br>Facultad de Bioquimica y Cs. Biológicas<br>Universidad Nacional del Litoral<br>Santa Fe - Argentina<br>C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA<br>Argentina<br>Ph. +54 (342) 4575-213<br>Fax. +54 (342) 4575-221 </i></font></div></div></div>