[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
>this.
>
>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.
>
>Thanks,
>
>Katherine
>
>--
>SIPPEL,KATHERINE H
>Ph. D. candidate
>Department of Biochemistry and Molecular Biology
>College of Medicine
>University of Florida
>
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