[Chimera-users] Measuring Distances in Chimera

Miguel Ortiz Lombardia miguel.ortiz-lombardia at afmb.univ-mrs.fr
Thu Jan 21 01:07:45 PST 2010

Dear Elaine,

Thank you for the procedures that you suggest. They are indeed useful!

Best regards,


Le 20 janv. 2010 à 19:00, Elaine Meng a écrit :

> Hi Miguel,
> There is no user interface one-step to do exactly that, but here are a couple of ideas:
> (a) if you are handy with python, you could get a list of the atoms within a zone of "atom1" and then loop through that list, creating their distance measurements to "atom1"
> (b) here is what I'd do, as a nonprogrammer: instead use "Find Clashes/Contacts" (under Tools... Structure Analysis) or the command equivalent, "findclash".  It can write out a list of atom pairs meeting your criteria, their distances, and their VDW overlaps (which can be negative, corresponding to when the VDW spheres of a pair of atoms are not overlapping but separated by space).   The cutoff you give this tool is actually the VDW overlap rather than the distance, but if it is really distances you care about, you can set the cutoff VDW overlap generously to include the distances you want, then sort the output by the distances.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> For example, the findclash command in the following:
> open 2gbp
> preset apply int 2
> show ligand z<8
> focus
> findclash :bgc at o1 overlap -1.0 hbond 0.0 log true
> ... finds all atoms in other residues interacting with BGC atom O1 (with their VDW surfaces within 1 Angstrom) and writes the following information to the Reply Log:
> Allowed overlap: -1
> H-bond overlap reduction: 0
> Ignore contacts between atoms separated by 4 bonds or less
> Ignore intra-residue contacts
> 8 contacts
> atom1  atom2  overlap  distance
> BGC 310.A O1  ASP 154.A OD1  0.231  2.649
> BGC 310.A O1  ASN 256.A ND2  -0.005  3.105
> BGC 310.A O1  ARG 158.A NH2  -0.154  3.254
> BGC 310.A O1  ASP 154.A CG   -0.272  3.612
> BGC 310.A O1  ASN 91.A ND2   -0.275  3.375
> BGC 310.A O1  HOH 319.A O    -0.677  3.597
> BGC 310.A O1  HOH 379.A O    -0.782  3.702
> BGC 310.A O1  ASP 154.A CB   -0.887  4.227
> The last column is the distance. There are also options for saving the information to a file, whether pseudobonds should be drawn and their linewidth and color, etc. The graphical interface "Find Clashes/Contacts" has the same capabilities.  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 Jan 20, 2010, at 12:02 AM, Miguel Ortiz Lombardia wrote:
>> Hi,
>> Now that we're here... Is it possible to pick just one atom and show the distances of surrounding atoms within a certain radius. I'm not talking about zone selection, just showing distances (as the usual pseudo-bonds) up to a fixed or user-defined radius. If the possibility does not exist, it would be nice to have.
>> Best,
>> -- Miguel
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-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
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