[Chimera-users] measure volume for protein subsections

Tom Goddard goddard at sonic.net
Tue Apr 19 17:07:29 PDT 2011

Hi Anke,

   You can rotate and crop a volume created by a preceding rotation and 
crop operation.  Each time it interpolates the map on a new grid aligned 
with the new rotated axes.  So you could get some degradation in map 
quality.  To miminize that you could set the "sample at voxels size X" 
setting in the subregion selection panel to use a finer grid spacing 
than the original data. By default the value it uses is the same grid 
spacing as the original map.

   Multiple rotations and cropping just gets you the intersection of 
various rotated boxes.  That is always a convex region.  Maybe that is 
not adequate for your purpose.  Here are two more flexible approaches.  
You can use the Volume Eraser tool to simply erase the density outside 
the part of the monomer you want to measure.  That tool lets you erase 
density (set values to zero) inside a sphere whose size you control.  
You just move it around and carve out whatever region of density you 
want.  Then measure the volume enclosed by a surface for the resulting 
partially erased map.  A second approach is to trace a surface with the 
Volume Tracer tool by placing markers to draw paths and connecting the 
paths to form a surface.  Then you can use the Chimera "mask" command to 
extract just the region of the map inside (or outside) the surface, 
parts outside the surface being set to 0.  You can also use standard 
shapes like spheres, ellipsoids, cylinders, icosahedra to define the 
masking surfaces using the "shape" command.


> Hi Tom.
> This is very helpful, thanks so much.  Followup question:  Now let's say that my protein monomer is not sitting in a regular old bilayer, so that I will need to use multiple rotated box cropping rounds to segment out what I really want to measure--is there any issue with sampling that says I have to keep cropping from the original protein monomer, or can I do successive cropping on each resampled volume?
> Cheers
> a.
> On Apr 16, 2011, at 11:28 AM, Tom Goddard wrote:
>> 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
>>      http://www.cgl.ucsf.edu/chimera/videodoc/rotatedbox/
>> 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.
>>      Tom
>>> 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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> ------
> Anke M. Mulder, PhD
> Director, Research and Development
> NanoImaging Services, Inc.
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