Klaus,
I can only assume that the pointed comment below was directed at me so I'll reply. Oh no, everything matters. I was just giving an example of how to use the pymol command. What distance cutoff is ultimately used is up to the crystallographer and the problem at hand. Note also the potential for water-mediated bonds, etc, that would be missed. It really was just an example, and trying to give the poster of the question a starting point to explore.
Just one 'pharmaceutical' crystallographer's viewpoint.
Best regards,
Steve
-----Original Message-----
From: Klaus Futterer [mailto:[log in to unmask]]
Sent: Friday, September 21, 2007 5:06 AM
To: Soisson, Stephen Michael
Cc: [log in to unmask]
Subject: Re: [ccp4bb] How to calculate the contacts between the dimer-dimer interface
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/
---------------------------------------------------------------------
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
>
>
>
>
> ----------------------------------------------------------------------
> --------
> Notice: This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
> New Jersey, USA 08889), and/or its affiliates (which may be known
> outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
> and in Japan, as Banyu - direct contact information for affiliates is
> available at http://www.merck.com/contact/contacts.html) that may be
> confidential, proprietary copyrighted and/or legally privileged. It is
> intended solely for the use of the individual or entity named on this
> message. If you are not the intended recipient, and have received this
> message in error, please notify us immediately by reply e-mail and
> then
> delete it from your system.
>
> ----------------------------------------------------------------------
> --------
------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and then
delete it from your system.
------------------------------------------------------------------------------
