Dear Randy,
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!
I'm pretty sure its not actually full copies. The unit cell is
262.9, 262.9, 609.1 with an R32 space group. I'm downloading the
latest release at the moment.
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.
Thanks for the tips on the ASU, I wouldn't have thought of that.
can then expand the rest using standard icos symmetry.
I think the answer will be do what's easiest, and if it's 99% ID
it should >fall out pretty easily anyway. Bear in mind that
depending on what you've >done to these capsids the icos ASU's
may have slightly re-oriented (in my case >I had added a drug
Hi Katherine,
Back when I did this with HBV I had one capsid per
crystallographic AsU and I >used Amore (pre-phaser or phenix). I
searched with the icosohedral ASU >looking for 60 copies, and was
surprised how easily the solution fell out. If >you use this
strategy, you really just need one icos ASU per capsid and you
that kept the icos ASU identical but had tilted the whole >thing
relative to the plane of the capsid). This may also guide your
strategy.
Good luck,
Christina
Our standard protocol is Amore with CNS. When Amore failed I
thought I might try something different. I have really enjoyed
Phenix for my small proteins and thought that I might take
advantage of that lovely NCS feature in phenix.refine. I just
wasn't sure how to proceed within the AutoMR program. Obviously in
the end I will go with what works.
PS- Isn't Mavis around in Florida somewhere, or are you even in
her lab? She >and Rob are a great resource....
I do work for Rob and Mavis and they are a fabulous resource. Best
bosses ever (and no they won't see this, its just the truth).
Thanks for the help,
Katherine
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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--
SIPPEL,KATHERINE H
Ph. D. candidate
McKenna Lab
Department of Biochemistry and Molecular Biology
College of Medicine
University of Florida