VMD-L Mailing List

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Thu Feb 03 2005 - 07:52:00 CST

hi,

> You'd want to use the "measure contacts" command, described in the VMD
> User's guide. Given two selections, one for CL and one for protein,
> and a cutoff distance, it will give you lists of corresponding to all
> CL-protein pairs within that distance. You can then create another
> set of selections to extract the resid information.
thank you very much for your excellent hint, the script is great.
however there is still one question left. this script prints out all
atoms of the protein structure that are within the specified distance.
is there any way to simplify the output so, that all atom pairs
corresponding to the same pair of residues will be printed out only
once? i.e. instead of printing out 3 contacts of one chloride with 3
different atoms of 1 aminoacid, only 1 contact between resid of the
chloride and resid of the aminoacid will be printed out.

thanks for your help,
lubos 

-- 
Lubos
_@_"