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

[Tom Goddard]

Or you can try using the molmap command to make a density map from the atomic model.  If the atomic model is #0 then

	molmap #0 4

will simulate a density map at resolution 4 Angstroms.  Then you can color the contour surface of that density map.

	Tom


> On Sep 23, 2019, at 9:45 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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.
> 
> <https://www.ebi.ac.uk/pdbe/emdb/searchResults.html/?q=*virus*>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
> 
> 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.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
> 
> I hope this helps,
> Elaine
> -----
> 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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