Deep-View (Swiss PDB Viewer) allows to calculate (and visualise) a
'contact surface'
between two subunits, by loading the subunits into different layers.
Residues contributing to the contact surface can be selected by CTRL-
click
on the contact surface line in the 'Cavities' menu, available under
the 'Window' drop-down menu.
BTW: I'm wondering about the 4A cut-off. Do distances greater than
this not
matter anymore in the view of a 'pharmaceutical' crystallographer?
Klaus
---------------------------------------------------------------------
Klaus Fütterer, Ph.D.
School of Biosciences P: +44-(0)-121-414 5895
University of Birmingham F: +44-(0)-121-414 5925
Edgbaston E: [EMAIL PROTECTED]
Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/
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On 20 Sep 2007, at 20:29, Soisson, Stephen Michael wrote:
If you just want the residues involved in the interface, you can
use the
byres selection commands in Pymol.
select contacts, (byres monA and (monB around 4))
which will show all the residues on monA that are within 4 Ang. of Mon
B.
Steve
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Xiaoyi Deng
Sent: Thursday, September 20, 2007 1:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to calculate the contacts between the dimer-
dimer
interface
Dear all:
I used moleman2 to calculate the contacts between chain A and B. Can
anyone suggest a program to calculate the contacts between the
interface
of dimer-dimer?
Thank you,
Xiaoyi
Graduate student
University of Nebraska Medical center
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