[Chimera-users] measure volume for protein subsections

Anke Mulder MULDER at nanoimagingservices.com
Tue Apr 19 16:34:26 PDT 2011

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?


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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Email: mulder at nanoimagingservices.com

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