[Chimera-users] Chimera-users Digest, Vol 122, Issue 25

[Boaz Shaanan]

Hi Francesco,

I doubt that modeller knows how to take into account inter-subunit information. I would be surprised if it does. As far as I know, it's a sequence-homology based model building module which also uses fold recognition and probably other pieces of information but not about oligomeric arrangement. When I dealt with a similar problem (modelling a dimer) I modelled the subunit and then superimposed  each of the two subunits on top of the corresponding subunit of the known dimer, followed by Chimera's matchmaker. The resulting dimer is still considered   a hypothetical structure by me.  

  Cheers,

           Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





________________________________________
From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] on behalf of chimera-users-request at cgl.ucsf.edu [chimera-users-request at cgl.ucsf.edu]
Sent: Sunday, June 23, 2013 10:00 PM
To: chimera-users at cgl.ucsf.edu
Subject: Chimera-users Digest, Vol 122, Issue 25

Send Chimera-users mailing list submissions to
        chimera-users at cgl.ucsf.edu

To subscribe or unsubscribe via the World Wide Web, visit
        http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
or, via email, send a message with subject or body 'help' to
        chimera-users-request at cgl.ucsf.edu

You can reach the person managing the list at
        chimera-users-owner at cgl.ucsf.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Chimera-users digest..."


Today's Topics:

   1. modeling multimers (Francesco Pietra)
   2. Fwd: modeling multimers (Francesco Pietra)


----------------------------------------------------------------------

Message: 1
Date: Sun, 23 Jun 2013 07:17:44 +0200
From: Francesco Pietra <chiendarret at gmail.com>
To: chimera <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] modeling multimers
Message-ID:
        <CAEv0nmt6Sy2MJcs=xk18qMGs2d5h0QOS_i7YXAJ1AEwpdWWsCQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello:
Modeling a trimer (all three chains present, though missing residues and
atoms) with chimera and modeller installed locally.

The default is modeling each chain, one at a time. The chains are identical
in sequence but the X-ray structure shows different localized
conformations. Question: is modeller modeling by taking the other two
chains into account?

If already answered, beg pardon.

thanks

francesco pietra
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130623/cba478c6/attachment-0001.html>

------------------------------

Message: 2
Date: Sun, 23 Jun 2013 11:13:21 +0200
From: Francesco Pietra <chiendarret at gmail.com>
To: chimera <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Fwd: modeling multimers
Message-ID:
        <CAEv0nmu9iHdkLX+wfozEiHoSi7iNht68FR2XdwYjgA9ptrWZTA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

If not clear, the template here is the fasta file. I wonder where Sali's
modeller allows filling residues in a multimer by also taking into account
the inetraction between the different subunits. Not seen any example.
francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Sun, Jun 23, 2013 at 7:17 AM
Subject: modeling multimers
To: chimera <chimera-users at cgl.ucsf.edu>


Hello:
Modeling a trimer (all three chains present, though missing residues and
atoms) with chimera and modeller installed locally.

The default is modeling each chain, one at a time. The chains are identical
in sequence but the X-ray structure shows different localized
conformations. Question: is modeller modeling by taking the other two
chains into account?

If already answered, beg pardon.

thanks

francesco pietra
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130623/c260d586/attachment-0001.html>

------------------------------

_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


End of Chimera-users Digest, Vol 122, Issue 25
**********************************************