[phenixbb] AutoMR and capsids

Randy J. Read rjr27 at cam.ac.uk
Thu Oct 22 11:06:44 PDT 2009

Dear Katherine,

If you're sure that there are 3 full copies (and that you couldn't, say, 
have six half-copies sitting on crystallographic 2-folds), the best would 
be to search for full capsids. Now, for each copy there are 60 different 
ways that the capsid could be oriented, but the version of Phaser 
distributed with the latest Phenix release should recognize the internal 
symmetry -- let us know if it doesn't!

If it turns out that a capsid is sitting on a symmetry axis, Phaser will 
probably reject it because of an outrageous number of clashes. In that 
case, you should turn off the clash test, just look for one copy, and then 
examine the overlapped solution to see which part of the capsid is 
crystallographically unique.

Good luck!

Randy Read

On Oct 22 2009, SIPPEL,KATHERINE H wrote:

>Dear all,
>I am currently trying to use AutoMR to do molecular replacement on 
>an icosahedral virus capsid. It is a T=1 capsid so there are 60 
>copies of the monomer per capsid and based on the Matthews 
>coefficient there are ~3 capsids in the unit cell. The search 
>model is 99% identical (thank God) but I am unsure how to approach 
>Do I used the 60-mer as the model and search for three copies? Do 
>I use a monomer for the model and search for 180 copies? Should I 
>break the model down to smaller pieces (i.e. a 30-mer and 
>copies=6, or 12-mer and copies=15)?
>I would appreciate any help I can get on this one.
>Ph. D. candidate
>Department of Biochemistry and Molecular Biology
>College of Medicine
>University of Florida
>phenixbb mailing list
>phenixbb at phenix-online.org

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