[Chimera-users] Create an entire virus from Octant

Li, Zongli Zongli_Li at hms.harvard.edu
Mon Mar 27 20:18:03 PDT 2017

Hi Tom,

Thank you so much for your help, really appreciate.



From: Tom Goddard <goddard at sonic.net>
Sent: Monday, March 27, 2017 7:42:35 PM
To: chimera-users at cgl.ucsf.edu BB
Cc: Li, Zongli
Subject: Re: [Chimera-users] Create an entire virus from Octant

Hi Zongli,

  Assign icosahedral symmetry to the map using the BIOMT matrices in the fit PDB coordinates then use vop cover to extend the octant map using that symmetry:

open emdbID:5199
open 4v7q
volume #0 symmetry #1
vop cover #0 ibox -499,-499,-499,499,499,499 cellsize 2000,2000,2000

The octant map is size 500,500,500 and I assume the 0,0,0 grid point is at the center of symmetry so the vop cover command says to cover grid points -499 to 499.  The vop cover command is intended to be used with crystallography so I also tell it the unit cell is bigger than the full map (2000 instead of 1000) so it does not use periodicity of the map.  The vop command took about 45 minutes to execute — very slow.

  The result of this symmetric covering is not ideal because the edges of the octant map could introduce artifacts in the full map.  Also it is interpolating the one octant at all symmetry equivalent points and averaging, and this trilinear interpolation is going to introduce a little bit of blurring.  Unfortunately because of the symmetry you can’t simply put 8 copies of the octant map together to form a full virus.  The x,y,z axes are 2-fold symmetry axes so the given octant can be mapped to 4 of the 8 octants with no grid interpolations, but the other four require other symmetry operators, not just 90 degree rotations.  So you can’t reproduce the full virus map with complete fidelity.  The only way to avoid the interpolation is to get a full map from the Harrison lab.  It is unfortunate that only this inadequate octant map is what is in the EMDB.  In the attached image I show the EMDB 5199 octant, and a neighbor octant which obviously is not just a rotated copy since the original octant has 9 spikes while the neighbor octant has only 6.


[cid:FE798923-04E2-46DF-B9F1-CDE4D99131FF at cgl.ucsf.edu]

On Mar 27, 2017, at 9:49 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

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<mailto:Zongli_Li at hms.harvard.edu>> wrote:

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?

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