VMD-L Mailing List

From: syma (syma.khalid_at_bioch.ox.ac.uk)
Date: Wed Nov 02 2005 - 11:47:48 CST

Hi,

I've attached a script that I have taken from the vmd mailing list- WED 02
2005 - submitted by Mgr Lubos Vrbka.

The script produces 4 files detailing the number of contact between two
selections over a trajectory. The two files I am interested in are
contact_A.dat and contact_B.dat. I was wondering if I could get some advice
on how to modify the script so that all the residues in eg a protein a
printed, not just the ones that actually make contact. So if there is no
contact with a certain resdiue then to print the residue number, residue
name and '0' for the number of contacts rather than just ignore it.

My ultimate aim is to use the number of contacts to colour the protein, ie
substitute no of contacts in the B factors column.

Thank you

-Syma

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Dr Syma Khalid
Department of Biochemistry,
University of Oxford
South Parks Road,
Oxford
OX1 3QU
U.K.

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