[Chimera-users] Create an entire virus from Octant

Li, Zongli Zongli_Li at hms.harvard.edu
Mon Mar 27 12:51:51 PDT 2017

Hi Elaine,

Thank you so much for the help. I look up the original post answered by Tom, as he pointed out, "The tricky part will be to assign the correct center of symmetry and icosahedron orientation for the asymmetric piece using the origin and symmetry options of the volume command". He is very right and I could not figured out the way to assign the correct center of the symmetry and icosahedron orientation for asymmetric piece with volume command while I am using "cop cover". The map I tried is EMD-5199 (rotavirus). Could you please help me out?

Thanks again,


From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, March 27, 2017 12:49:58 PM
To: Li, Zongli
Cc: chimera-users at cgl.ucsf.edu Mailing List
Subject: Re: [Chimera-users] Create an entire virus from Octant

Hi Zongli,
I believe you can use “vop cover” to expand the map if you can supply the needed symmetry information and box size.  Please see this previous post:


I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 26, 2017, at 8:01 PM, Li, Zongli <Zongli_Li at hms.harvard.edu> wrote:
> Hello,
> I am wonder if there is a way in Chimera to create an entire icosahedral virus map from an octant of the virus density map?
> Thanks,
> Zongli

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