[chimerax-users] measure volume using radii

[Elaine Meng]

Hi Heather, 
I'm not the one who figured out the recipe for capsid inside volume calculation; all credit goes to Tom G, who also put the example on github:
<https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html>

There is no command to set the contour level to give a certain surface "radius" (in quotes since it's still an irregular shape, rather than a sphere or other idealized solid).  Maps don't have surface coordinates per se, they just have values on a grid in 3D and the surface is merely a contour of the specified level relative to those values.  As you saw, the surface will move around and change shape depending on how you set the contour level.

Although the volume command has an "encloseVolume" option to set the contour level to enclose a specific total volume, that would be the volume between the inner and outer surfaces, not inside the inner surface.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#encloseVolume>

There is no recommended contour level across maps.  Different maps have different levels of noise and resolution.  Sometimes the map header in the file has a recommended level for that specific map, but I'm not the expert on how you would extract or use it.

If you just want to draw an ideal sphere or icosahedron surface, see the "shape" command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.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 Jul 19, 2022, at 5:19 PM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello Elaine,
> 
> I hope this email finds you well. I have a couple of questions for you. I have been working on the measurement of enclosed volumes, these are the commands I have been using:
> 
> molmap #1 12
> volume level 0.07
> "blob"
> surface splitbycolor #2.1
> view position #3 sameAs #2
> measure volume #3.2
> 
> I am curious if there is a command to change the map radius to:
> 
> outer radium: 145
> ave radium: 141
> inner radium:84
> 
> Or if you are aware of a map that already has these coordinates?
> 
> Lastly, for the volume level is there a default level that maybe is recommended once these radii are in place? The 0.07 level seems to render lower inner volumes (i.e. 2.348 x 10^6) compared to the one below for example.
> 
> I am going to attach one of my PDB files if you need it. The inner volume calculation through the review is 2.48 x 10^6 cubic angstroms, just as a reference for this file.  Thanks so much, and hope to hear soon.
> 
> Thank you,
> 
> Heather Noriega
> PhD-Pharmaceutical Science student 
> Howard University
> heather.noriega at bison.howard.edu
> 520-203-1883
>  AAV_3B_VP3_only.pdb