[Chimera-users] measure volume for protein subsections

Tom Goddard goddard at sonic.net
Sat Apr 16 11:28:39 PDT 2011

Hi Anke,

   You are right, Chimera does not know how to measure the enclosed 
volume within just a clipped portion of a surface.  It always reports 
the enclosed volume of the whole surface, including the part removed by 
the clip planes.  But it can be done by clipping in a different way.  
Here's how.

   First you need to be looking at a surface for a volume data set.  You 
can select the Segger region and use the Segment map dialog menu entry 
Regions / Mask Map with Selected to get a volume just for one monomer.  
Now use the volume dialog Subregion Selection panel (under Features 
menu), enable selecting subregions with mouse and drag a green outline 
box with the middle mouse button over the monomer volume.  Click the 
"rotate selection box" button and align the green outline box with the 
lipid bilayer.  You can adjust the box size by dragging the faces of the 
box with the middle mouse button. Then use the crop button to crop the 
volume to just that box.  You can then measure the enclosed volume for 
that cropped volume.  Here's a video that shows the rotated box cropping


If you prefer to get the volume in the lipid layer for an atomic model 
you can use the "molmap" command to make a density map from the atomic 
model and use the same procedure.

   I''ll put in a feature request for measuring volume with proper 
accounting for the clip planes.


> Hi,
> I have used segger to divide my reconstruction into protein monomers, and I know how to measure the volume and other attributes of the protein monomer, however, I would like to be able to measure subsections of the monomer so that I can have an idea of what the volume of protein is that, for example, is buried in the lipid bilayer, etc.  I thought that I could use clipping planes to do this, but from what I can tell the volume measurement still takes into account the volume of the entire protein.
> Thanks so much.
> Anke M.

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