VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jul 26 2007 - 11:48:08 CDT

On Thu, 26 Jul 2007, sfrickenhaus wrote:

stefan,

SF> I have the impression that the measure-gofr cannot filter for only
SF> displaying non-bonded distances.
SF> How can I make a selection1 selection2 that excludes bonds between sel1
SF> and sel2?
SF> Any way to modify the gofr.tcl for that?

the gofr plugin is (rightfully so) completely agnostic
to bonding and atom type etc. it only sees the coordinates
in the two selections. so the only way to handle your problem
is to try making your selections smarter, if that is not possible,
run multiple measure gofrs and sum/average them.

cheers,
   axel.

p.s.: if you would ask multiple questions in seperate e-mails,
it would be easier for people to follow the discussion
on the part(s) that interest them and not have all threads
rolled into one big pile. thanks.

SF> Best regards,
SF> Stephan
SF>
SF> PS: who wants to try the box, ask me for psf and pdb.
SF>
SF> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.