calculating virus surface in prep for radial color display
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.
Rob
[cid:image003.jpg@01D56FE1.62351B70] [cid:image004.jpg@01D56FE1.62351B70]
_________________________
Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe@pfizer.commailto:Robert.Gampe@pfizer.com [cid:image006.jpg@01D4D043.EB786830] _________________________
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!
D
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@pfizer.commailto:Robert.Gampe@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.
Rob
<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@pfizer.commailto:Robert.Gampe@pfizer.com <image005.jpg> _________________________
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participants (2)
-
David Bhella -
Gampe, Robert