[chimerax-users] measure volume using radii

[Noriega, Heather]

It definately does help. I had no idea Tom put the example up, but that is
good to know about the recipes. I will try the shape command and continue
to play with the level contour and higher resolution maps. Thanks so much 😊

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
College of Pharmacy
Howard University
heather.noriega at bison.howard.edu
520-203-1883

On Tue, Jul 19, 2022, 8:39 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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