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

[Gampe, Robert]

Hi Chimera Users

This is 2nd send to you after I enrolled as a CHIMERA user :), 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:

  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.

Rob



[cid:image001.jpg at 01D56FEE.1FF9C5A0][cid:image002.jpg at 01D56FEE.1FF9C5A0]


_________________________

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>
[cid:image006.jpg at 01D4D043.EB786830]
_________________________

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190921/a2ab739c/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 22786 bytes
Desc: image001.jpg
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190921/a2ab739c/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.jpg
Type: image/jpeg
Size: 2387 bytes
Desc: image002.jpg
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190921/a2ab739c/attachment-0001.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image003.jpg
Type: image/jpeg
Size: 4389 bytes
Desc: image003.jpg
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190921/a2ab739c/attachment-0002.jpg>