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@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@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@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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