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Have you used PISA - that generates all likely oligimersand allows you to download them.
Eleanor

On 19 November 2015 at 21:35, Jose Duarte <[log in to unmask]> wrote:
You can use the EPPIC server http://www.eppic-web.org, which will list all crystal contacts present in the lattice. Is that the kind of thing that you are looking for?

If you really want to get into the coding and do some more powerful things, under the hood it's all based in Biojava (https://github.com/biojava). You could check it out and play with the code to generate symmetry mates and do other things with contacts and interfaces.

Jose


On Thu, Nov 19, 2015 at 12:45 PM, Edward Snell <[log in to unmask]> wrote:

PS. Shameless plug: The program for the Gordon Research Conference on Diffraction Methods in Structural Biology (Probing the Structure and Dynamics of Macromolecules) will be available after the end of the month. This will be its 40th anniversary and we’re making it a good one. Save the date, JULY 17th-22nd, 2016.

 

Edward Snell Ph.D.

CEO Hauptman-Woodward Medical Research Institute

Assistant Prof. Department of Structural Biology, SUNY Buffalo

700 Ellicott Street, Buffalo, NY 14203-1102

Phone:     (716) 898 8631         Fax: (716) 898 8660

Skype:      eddie.snell                 Email: [log in to unmask] 

 

Heisenberg was probably here!

 

From: Edward Snell
Sent: Thursday, November 19, 2015 3:30 PM
To: [log in to unmask]
Subject: Generating alternative oligomer mates from a PDB structure

 

Dear CCP4,

 

Five days in a lab saves an hour in the library and I figuratively decided to follow that advice before I dust of my rusty coding skills.  Given an existing PDB does anyone know of a utility or have some useful code that could generate alternative symmetry mates for oligomers? As an example, if I have a dimer presented as a biological unit in the PDB I would like to be able to pull out all possible dimers independent of the one already defined. I’m looking at this as a trivial exercise, not any complicated means of accomplishing it. While it’s easy to do this one at a time, it gets more time consuming with a larger number. There is a practical purpose!

 

Any help is appreciated,

 

Thanks,

 

Eddie

 

PS. Shameless plug: The program for the Gordon Research Conference on Diffraction Methods in Structural Biology (Probing the Structure and Dynamics of Macromolecules) will be available after the end of the month. This will be its 40th anniversary and we’re making it a good one. Save the date, ***June**** 17th-22nd, 2016.

 

Edward Snell Ph.D.

CEO Hauptman-Woodward Medical Research Institute

Assistant Prof. Department of Structural Biology, SUNY Buffalo

700 Ellicott Street, Buffalo, NY 14203-1102

Phone:     (716) 898 8631         Fax: (716) 898 8660

Skype:      eddie.snell                 Email: [log in to unmask] 

 

Heisenberg was probably here!