[Chimera-users] calculation of volume

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 13 12:29:31 PDT 2008

Hi Navnit,
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:
      surf ligand
(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- 
binding protein).

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:
      surf :7-29.b
(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
      surf myligand
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  
volume lines.

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  
> first
> 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  
> like
> to calculate the molecular volume from amber trajectory. Can some one
> suggest me how to automate the computation of surface area and  
> molecular
> volume for each snapshot. If you know, please point out the article
> which describes the procedure for the volume calculation.
> with regards,
> Navnit

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