[Chimera-users] calculation of volume
meng at cgl.ucsf.edu
Wed Aug 13 12:29:31 PDT 2008
I see three parts to your question.
(1) how to surface the ligand and control what is enclosed in a surface
(2) how to get the volume enclosed in a surface
(3) how to repeat those things for each step of an MD trajectory
(1) You don't need any extra parameters. The default is to surface
"main," basically what is not solvent, ions or ligand by these
You can surface anything that is made of more than one atom, but
details of how to do it depend on the input structure. If your ligand
is already automatically classified as "ligand" by Chimera according
to those definitions, you can simply use the command:
(or equivalently, use "Select... Structure... ligand" and "Actions...
Surface... show" in the menu)
For example, this works for the ligand glucose in PDB 2gbp (glucose-
If your ligand is not already automatically classified as ligand, try
specifying it by residue name(s) or number(s) or chain ID, say with a
command something like:
(example structure 2cmy, where chain A is trypsin and chain B is a
smaller peptide, part of an inhibitor. I want to surface
the inhibitor, but "ligand" just includes some sulfates and detergent.)
Check to see that the surface completely encloses what you want. If
not, like in my example, it may be that your ligand was automatically
included with "main" instead of surfaced separately. Again you can
get what you want, now by telling Chimera that this should have its
own separate surface:
surfcat myligand :7-29.b
A similar procedure can be used when you want separate surfaces for
different chains when by default they are lumped together.
(2) Now that you have the surface you want, calculate the volume
inside of it with "Measure Volume and Area" (under Tools... Surface/
Binding Analysis). In my 2cmy example, all I have to do is choose
"MSMS myligand surface..." (or whatever name you used in the "surfcat"
command) from the Surface menu in that tool. In this case you would
not want the "ligand surface" because it refers those sulfates and
detergent molecules, but you would want "ligand surface" when "ligand"
correctly refers to the surface you want. The volume and area are
reported in the Reply Log (under Favorites).
(3) The preceding steps could be done on a single frame of your
trajectory being shown in MD Movie.
With "Update automatically" turned on in Measure Volume and Area, I
would then Clear the Reply Log, go directly to Frame 1 (by editing the
Frame value in MD Movie), in MD Movie, turn off "Loop" and then play
the trajectory to the end. All the volume values will be reported in
the Reply Log. You could Save the Reply Log contents to a file for
further text processing. For example, on unix you could grep out the
MD Movie also allows definition of per-frame scripts to do things at
each frame, but in this case it is not necessary to use that mechanism
since the volume-measuring tool can do automatic updates.
There are couple more issues relating to surface and volume
(A) the surface calculation fails on some structures, and this might
happen in some steps of your trajectory
(B) you can control the fineness of triangulation, probe radius, etc.
This will affect the volume results. To adjust these values: Ctrl-
click the surface to select it, open the Selection Inspector
(Actions... Inspect), Inspect "MSMS surface", edit the values.
Higher vertex density (more triangles) gives a smoother surface and a
volume more like the analytical value, but makes the calculation
slower and might increase the failure rate. You may want to
experiment. If you do have failures, you may be able to avoid them by
changing vertex density and/or probe radius, or removing hydrogens if
they are not important for what you want to show.
I hope this helps,
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Aug 13, 2008, at 7:56 AM, Navnit Kumar Mishra wrote:
> Hello all;
> I am trying to compute the molecular volume of a complex. Chimera
> computes solvent-excluded surface area using MSMS. I see it does not
> compute the surface area of ligand. I am wondering if I can add the
> extra parameters or atom types for my ligand in some file. I would
> to calculate the molecular volume from amber trajectory. Can some one
> suggest me how to automate the computation of surface area and
> volume for each snapshot. If you know, please point out the article
> which describes the procedure for the volume calculation.
> with regards,
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