[Chimera-users] distance measurement

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 30 16:02:25 PST 2007

Hi Marco,
Here is a better example for your situation.  Instead of looking at all 
distances from one atom, this would look at all distances among the 
specified set of atoms, in this case hydrogens.

open 1zik
delete solvent
findclash element.H inter false overlap -3 hbond 0 makePseudobonds 
false log true

(where that findclash command is all on one line even though the mail 
reflector will probably break it up)  That finds all H pairs within 5 
angstroms, I believe.  That is very many pairs, even in this relatively 
small structure.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 30, 2007, at 3:47 PM, Elaine Meng wrote:

> Hi Marco,
> Pardon the delay - at first I thought it was not possible with a
> command to measure multiple distances and that somebody else would have
> to give you a script.
> However, it IS possible, but not with the "distance" command.  The
> "findclash" command (or Find Clashes/Contacts tool) can find all
> clashes or contacts within some user-specified tolerance and write the
> results to a file. The cutoff is how much VDW overlap is present, but
> setting that cutoff to a negative number (with H-bond tolerance of
> zero) will find pairs of atoms with VDW surfaces within the cutoff
> distance ( its absolute magnitude).  The distances between the atom
> centers will be greater than that, but the information written to the
> file or to the Reply Log includes the distances between atom centers as
> well as between the VDW surfaces.  Just be forewarned that this may be
> a LOT of lines depending on your system and specified cutoff.
> It's a little confusing, but here is an example:
> open 1zik
> findclash :23.a at cg2 overlap -5 hbond 0 ignoreIntraRes true log true
> will draw lines in the graphics window and send information to the
> Reply Log on all pairwise interactions where the VDW surface of atom
> CG2 in residue 23 chain A is within 5 angstroms of the VDW surface of
> the other atom.  The lines are sorted in order of decreasing overlap:
> atom1  atom2  overlap  distance
> VAL 23.A CG2  VAL 23.B CG2    0.707  3.053
> VAL 23.A CG2  LEU 19.A O      0.225  3.075
> VAL 23.A CG2  VAL 23.B CB     -0.631  4.391
>   ...
> VAL 23.A CG2  ARG 25.B NH1    -4.882  8.402
> VAL 23.A CG2  LYS 27.B N      -4.937  8.457
> Including "saveFile filename" will save the information to a text file
> named filename.  You can do exactly the same thing via the Find
> Clashes/Contacts GUI instead of the "findclash" command.
> Here is the man page for findclash ...there are many possible keywords:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html
> and for Find Clashes/Contacts:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/
> findclash.html
> On Nov 30, 2007, at 1:54 AM, sette at uniroma2.it wrote:
>> Or all the distances between less than 5-6 Angstrom from atom A.
>> It would be nice if this could be written to a file.
>> I'm analysing a NMR NOESY spectrum of DNA and I would like to have a
>> list of the expected distances in typical B-DNA.
>> Thanks,
>> Marco

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