[Chimera-users] map sigma

[Dieter Blaas]

Dear Elaine,

     Thank you again! Unfortunately the meaning of 'sigma' in this 
context is still not clear to me [see e.g. Fig. 4 in  A. Bennett et al., 
Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2. 
J Struct Biol 209, 107433 (2020)]. In this figure they show a density 
map at sigma=1, sigma=2, and sigma=3, which is reflected in an the 
expansion of the map, i.e. in a DECREASE of the numerical value of the 
contour level. However, when I use these same values for sdLevel (i.e. 
vol #0 sdLevel 1, vol #0 sdLevel 2, and vol #0 sdLevel 3) I see the 
contrary i.e. the map is shrinking (i.e. an INCREASE of the contour 
level values of 0.00165, 0.0033, 0.00496, respectively). So, what do I 
misunderstand? How are 'sdLevel' and 'rmsLevel' correlated with 'sigma'?

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 20:08, Dieter Blaas wrote:
> 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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