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: [log in to unmask]
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:[log in to unmask]] On Behalf Of
> Xiaoyi Deng
> Sent: Thursday, September 20, 2007 1:26 PM
> To: [log in to unmask]
> 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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