[phenixbb] AutoMR and capsids

Christina Bourne bournecr at yahoo.com
Thu Oct 22 11:16:20 PDT 2009

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 strategy.
Good luck,

PS- Isn't Mavis around in Florida somewhere, or are you even in her lab?  She and Rob are a great resource....

From: "SIPPEL,KATHERINE H" <ksippel at ufl.edu>
To: phenixbb at phenix-online.org
Sent: Thu, October 22, 2009 11:08:40 AM
Subject: [phenixbb] AutoMR and capsids

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

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