[Chimera-users] measure volume for protein subsections

[Tom Goddard]

Here are some instructions for erasing parts of a volume and also for 
masking a volume to a surface

     
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#handerase

     
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#mask

   Tom



> 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.
> 11099 N Torrey Pines Road, Ste. 250
> La Jolla, CA 92037
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> Mobile: 619.309.5779
> Email: mulder at nanoimagingservices.com
>
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