[Chimera-users] map sigma

Dieter Blaas dieter.blaas at meduniwien.ac.at
Thu Mar 5 11:08:46 PST 2020

Dear Elaine,

    this is exactly what I was looking for, thank you!

bw Dieter

Dieter Blaas,
Max Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Mobile: 0043 699 1942 1659
e-mail: dieter.blaas at meduniwien.ac.at

On 05.03.2020 18:46, Elaine Meng wrote:
> Hi Dieter,
> I changed the Subject line to this new subject.
> How to “get" sigma is still the same as discussed in that message: you would either divide by the std dev before or after subtracting the mean, depending on your definition of sigma, and the mean and std dev can be reported with the "Volume Mean, SD, RMS” tool or command “measure mapStats”
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volstats.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapStats>
> However, you can specify threshold directly using either of these definitions with the volume command “rmsLevel” and “sdLevel” options.  That will not change the values shown in the data histogram in Volume Viewer, it will merely do the calculation and set the thresholds accordingly.   Example:
> volume #4 sdLevel 1.5
> For description of these options, see:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Mar 4, 2020, at 10:15 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
>> Dear Elaine, thank you and please forgive me still another question: Was there any followup on this?
>> http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html
>> I am wondering how the sigma can be determined correctly from the level value in the Volume Viewer and the outputs from Tools > Volume Mean, SD, RMS and, eventually, from Measure Volume and Area.
>> Is there now a way of getting the sigma directly?
>> Thank you very much, bw Dieter

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