[Chimera-users] distance measurement

[Elaine Meng]

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

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.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
>
>
> Citando sette at uniroma2.it:
>
>>
>> Dear all,
>>
>> I would like to measure the distances between all atoms in a molecule,
>> in particular between all hydrogens. I added the H but it seems to me
>> that is possible to measure only the distance between two selected
>> atoms and not between all atoms in a single command.
>> How is possible to do?
>>
>> Thanks for your help,
>>
>> Marco
>>
>>
>>
>>
>> Dr.Marco Sette, Ph.D.
>>
>> Department of Chemical Sciences and Technology
>> University of Rome, "Tor Vergata"
>> via della Ricerca Scientifica, 00133, Rome, Italy
>> e-mail:        sette at uniroma2.it
>> Tel.:          +39-0672594424
>> Fax:           +39-0672594328
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>
>
> Dr.Marco Sette, Ph.D.
>
> Department of Chemical Sciences and Technology
> University of Rome, "Tor Vergata"
> via della Ricerca Scientifica, 00133, Rome, Italy
> e-mail:        sette at uniroma2.it
> Tel.:          +39-0672594424
> Fax:           +39-0672594328
>
>
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