[Chimera-users] measuring multiple distances at once

Elaine Meng meng at cgl.ucsf.edu
Wed May 28 09:29:37 PDT 2014


Hi Marco,
Yes, you can even do it in a single step, but not with the distance command, which takes only two things at a time (two atoms, or one atom and one axis, etc.):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>

To get multiple atom-atom distance measurements at once you would use Find Clashes/Contacts (in menu under Tools... Structure Analysis) or the "findclash" command.  Although the cutoff you specify is the VDW overlap (distance between surfaces of VDW spheres, which can be positive or negative), it will output not only the overlaps but also the center-center distances.  The output can be written to Reply Log or to a file.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>

For example, to measure distances between atoms named HN in model #0 and nearby atoms named HA in model #1:

findclash #0 at hn test #1 at ha overlap -4 hbond 0 log true

would find all HN-HA pairs with VDW surfaces within 4 angstroms of each other (make sure those are the correct atom names, and you could use larger negative cutoff to find pairs farther apart) and write all the overlaps and center-center distances of those pairs to the Reply Log.  There's another example in this previous post:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008741.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 28, 2014, at 3:14 AM, sette at uniroma2.it wrote:

> Hi Elaine,
> thanks a lot.
> It is possible, in the last version to measure distances from one (or more) single atoms and other groups of atoms?
> for example HN of a protein and ha of that proteins?
> Thanks,
> Marco




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