[Chimera-users] square of density volume

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 9 10:04:35 PDT 2010

Hi Ryo,
Sorry, I don't think there is any tool or command that will square all  
the values in a map.

The volume-editing command "vop" has several options for different  
kinds of smoothing and scaling the values by a constant, but not  
squaring them:

Also, there is a "Volume Mean, SD, RMS" tool but it just gives one  
value of mean, etc. for the whole map:

I'm sure it could be done with a python script in Chimera, but that is  
beyond my skills.  Maybe when our volume expert gets back next week,  
he will have some suggestions.
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 9, 2010, at 1:38 AM, 仁田 亮 wrote:

> Hi chimera users,
> I want to calculate the square value for the volume of the electron  
> density because I want to calculate the variance map.
> Do anyone know whether we can calculate the square value of the  
> volume by chimera?
> And if we can, could you teach me how to calculate?
> Thanks for your time and help,
> Ryo

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