[Chimera-users] Print selected

m.maletta at nki.nl m.maletta at nki.nl
Mon Apr 28 05:23:23 PDT 2014

Dear Elaine,
Thank you a lot for your help.
It really worked perfectly. 
I changed the radius of all the atoms with vdwdefine so that only the distance from the center matter.

Massimiliano Maletta
post-doc in
NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam
group of Peter Peters
www.nki.nl/research/peters/   | www.necen.nl
m.maletta at nki.nl
Tel : +31 20 512 2022
Fax : +31 20 512 2029
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Friday, 25 April 2014 10:52 PM
To: Massimiliano Maletta
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Print selected

Dear Max,
The best way is to use the Find Clashes/Contacts tool (in menu under Tools... Structure Analysis) or its command version "findclash".  Either way you can define two sets of atoms, chain A and chain B in your case, and a cutoff distance, and then get a list of the distances saved to a file or to the Reply Log.  The cutoff you specify is not center-to-center distance, but "overlap" = the overlap between the surfaces of the VDW spheres, where 0 is exactly touching, positive is intersecting, negative is the separation of the VDW surfaces. Nevertheless the list of pairwise atom-atom results will include both the overlap values and the center-to-center distances, and if you really prefer the strict center-to-center distance cutoff, you can (manually) filter the results by that criterion.

For example, commands including option to write results to the Reply Log:

open 1zik
preset apply int 2
findclash :.a&protein test :.b&protein overlap -0.5 hbond 0.0 log true

The command has several options including "saveFile" as an alternative to "log", selecting the atoms, and drawing lines.  The center-to-center distances are the last column in the results.  To get larger distances you would use a larger negative overlap cutoff.

The graphical interface (Find Clashes/Contacts tool) can do the same things.  It is fairly self-explanatory, but to define two sets of atoms you'd first select one set, then "Designate", then select the second set and "Designate... as second set":

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 Apr 25, 2014, at 5:13 AM, <m.maletta at nki.nl> <m.maletta at nki.nl> wrote:

> Dear all,
> I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds.
> I manage to do the first part with this command, but I do not manage to have a list of all the distances found.
> select #0:.A za<3.5 & #0:.B
> Is there a way to get the list?
> Best and thank you in advance
> Max

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