[phenixbb] AutoMR and capsids
ksippel at ufl.edu
Thu Oct 22 16:00:13 PDT 2009
> 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.
> 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
> >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
> that kept the icos ASU identical but had tilted the whole >thing
> relative to the plane of the capsid). This may also guide your
> Good luck,
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,
> 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.
>> SIPPEL,KATHERINE H
>> Ph. D. candidate
>> Department of Biochemistry and Molecular Biology
>> College of Medicine
>> University of Florida
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
Ph. D. candidate
Department of Biochemistry and Molecular Biology
College of Medicine
University of Florida
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