[chimerax-users] measure volume using radii

[Elaine Meng]

Hi Heather,
I realized that since you are simulating a map from atomic coordinates (which is what "molmap" does), what I said about experimental maps is not so relevant, namely to consider their differing levels of noise and resolution, and that their authors may supply recommended threshold levels.

In your case, it is important to realize that this recipe for volume calculation is approximate, almost back-of-the envelope.  Although you may get a precise-looking number with lots of digits, don't let it make you think that the calculation method is precise.    Ideally one would use the molecular surface instead of molmap isosurface, but if I remember correctly, that does not work for blob separation because of holes and interconnections.  Thus we had to resort to a lower-resolution (and thus smoothed or smeared out) surface such as from a low-resolution molmap.  These choices are all due to the limitations of how we can calculate the volume in ChimeraX.

I don't know what you mean by "through the review" ... if you meant that somebody else who wrote a review said that that was the volume, then what matters is how they calculated the volume.  You couldn't really expect to get exactly the same value unless you used the same method.  If you meant that the volume from the review was a value that you calculated earlier, then if you want to compare between different PDB files, you should use the same method, including the same molmap resolution value and the same map isosurface level for all of the PDB files. Just because you can achieve a different calculated inner volume by using a different map level, it does not alter the (relative) reality of the atomic positions in that PDB file.  Keeping the parameters the same should help in keeping the relative sizes consistent when comparing between different PDB files.  However, as to whether any single volume measurement is "the truth" depends on how you define the truth (how to treat holes and bumps in the molecular surface, how similar the molmap surface is to the molecular surface).

If this multistep ChimeraX method is too problematic (fails in some of your structures), then you may need to use a different method, possibly different program(s) or your own code.

I hope this clarifies the situation,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 19, 2022, at 5:39 PM, Elaine Meng via ChimeraX-users <chimerax-users 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