[Chimera-users] calculating virus surface in prep for radial color display

David Bhella David.Bhella at glasgow.ac.uk
Tue Sep 24 00:42:14 PDT 2019

The figure you shared looks more like the cryoEM map than a surface generated from a pdb file.
Why not download a map from EMDB?
There are several AAV maps, I made the attached image using EMD6470.
Looks even better in ChimeraX!


David Bhella

Professor of Structural Virology
Associate Director - MRC-University of Glasgow Centre for Virus Research
Director - Scottish Centre for Macromolecular Imaging

Sir Michael Stoker Building
Garscube Campus
464 Bearsden Road
Glasgow G61 1QH
Scotland (UK)

Telephone:  0141-330-3685
Skype: d.bhella

On 20 Sep 2019, at 23:29, Gampe, Robert <Robert.Gampe at pfizer.com<mailto:Robert.Gampe at pfizer.com>> wrote:

Hi Chimera Users

I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below.

However the:

  1.  Action, Surface, Show

command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ).

Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn’t see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed.

Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below.

Any solutions greatly appreciated and thanks.


<image003.jpg> <image004.jpg>


Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc.
7030 Kit Creek Rd, Morrisville, NC 27560
Office: 919-666-5969| Robert.Gampe at pfizer.com<mailto:Robert.Gampe at pfizer.com>

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