[Chimera-users] measure symmetry

[Tom Goddard]

Hi Reggie,

  You are right that the EMDB 1220 virus capsid has none of the standard icosahedral orientations. It is approximately 3-fold axis along z, and 2-fold axis along x (Chimera orientation 2n3r) but it is maybe 5 degrees off from that.  If this capsid was refined with C1 symmetry then there is no reason for it to have a standard orientation.  It will be difficult to compute the icosahedral symmetry matrices.  I suggest you talk to the author of that map Gabe Lander who has a lab at Scripps, right where you are located.

	Tom


On Oct 8, 2014, at 2:07 PM, Reginald McNulty wrote:

> Thanks. It works.
> I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map?
> Reggie
> On Oct 8, 2014, at 11:34 AM, Tom Goddard  wrote:
> 
>> Hi Reggie,
>> 
>>   I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached.
>> 
>> 	Tom
>> 
>> open 2xyz
>> rainbow chain
>> sym #0 surf true
>> 
>> # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation).
>> 
>> shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5
>> molmap #0 10 sym i,n25r
>> 
>> 
>> <2xyz.jpg>
>> 
>> On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote:
>> 
>>> Dear Tom,
>>> 
>>> I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts?
>>> I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html
>>> 
>>> All the best,
>>> -Reggie
>>> 
>>> --
>>> Reginald McNulty, Ph.D.
>>> Postdoctoral Research Associate
>>> The Scripps Research Institute
>>> Johnson Lab
>>> Department of Integrative Structural and Computational Biology 
>>> 10550, N. Torrey Pines Road, MB-31 
>>> La Jolla, California 92037
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
> 
> 

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