[Chimera-users] Measuring Distances in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 20 10:00:51 PST 2010

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.

For example, the findclash command in the following:

open 2gbp
preset apply int 2
show ligand z<8
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 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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