<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi Katherine,<br>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.<br>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.<br>Good
luck,<br>Christina<br><br>PS- Isn't Mavis around in Florida somewhere, or are you even in her lab? She and Rob are a great resource....<br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> "SIPPEL,KATHERINE H" <ksippel@ufl.edu><br><b><span style="font-weight: bold;">To:</span></b> phenixbb@phenix-online.org<br><b><span style="font-weight: bold;">Sent:</span></b> Thu, October 22, 2009 11:08:40 AM<br><b><span style="font-weight: bold;">Subject:</span></b> [phenixbb] AutoMR and capsids<br></font><br>
Dear all,<br><br>I am currently trying to use AutoMR to do molecular replacement on <br>an icosahedral virus capsid. It is a T=1 capsid so there are 60 <br>copies of the monomer per capsid and based on the Matthews <br>coefficient there are ~3 capsids in the unit cell. The search <br>model is 99% identical (thank God) but I am unsure how to approach <br>this.<br><br>Do I used the 60-mer as the model and search for three copies? Do <br>I use a monomer for the model and search for 180 copies? Should I <br>break the model down to smaller pieces (i.e. a 30-mer and <br>copies=6, or 12-mer and copies=15)?<br><br>I would appreciate any help I can get on this one.<br><br>Thanks,<br><br>Katherine<br><br>--<br>SIPPEL,KATHERINE H<br>Ph. D. candidate<br>Department of Biochemistry and Molecular Biology<br>College of Medicine<br>University of Florida<br><br>_______________________________________________<br>phenixbb mailing list<br><a
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