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

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 23 09:45:23 PDT 2019

Hi Rob,
It wasn’t necessary to send the question again — questions from people not yet signed up to the list will still appear on the list after the moderator approves them (if they’re clearly not spam).

Normally this type of radial coloring is done on a density map isosurface, not on a molecular surface calculated from the atomic positions, the kind of surface you were trying to show.

You can look for AAV electron microscopy maps at EMDB (I find 11 maps there for organism “adeno-associated virus") and choose one of them to show, adjust the isosurface in Volume Viewer if needed, and then use Surface Color for radial coloring.


In Chimera, you can fetch directly from EMDB using menu: File… Fetch by ID, choosing EMDB in the dialog and entering the ID, e.g. 0535

If you really want to use a specific atomic structure, you could instead try showing low-resolution “multiscale” surfaces for that atomic structure instead of the standard molecular surfaces that are prone to calculation failures.  Menu: Tools… Higher-Order Structure… Multiscale Models, and in that dialog click the “Make models” button near the bottom, then use Surface Color for radial coloring.


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

> On Sep 20, 2019, at 5:01 PM, Gampe, Robert <Robert.Gampe at pfizer.com> wrote:
> Hi Chimera Users
> This is 2nd send to you after I enrolled as a CHIMERA user J, thanks.
> 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:
> 	• 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. 
> Rob
> <image001.jpg><image002.jpg>

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