[Chimera-users] square of density volume

nittaryo at gmail.com nittaryo at gmail.com
Fri Apr 9 15:58:11 PDT 2010

Hi Elaine,
Thank you for your quick response.
I've already used several vop options which are very useful for  
my jobs.  If your volume experts have some useful ideas, I'm very  
happy to waiting for his comment next week.

On 2010/04/10, at 2:04, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>
> Also, there is a "Volume Mean, SD, RMS" tool but it just gives one  
> value of mean, etc. for the whole map:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volstats.html 
> >
> 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
> -----
> 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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