[Chimera-users] Question about unit of electron density

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 13 16:03:58 PDT 2014


Dear Matthias,
The level is according to the raw data, that is, the numbers in the input map file.  There is no automatic processing into sigma units.

You can calculate statistics for your map file using Tools… Volume Data… Volume Mean, SD, RMS, or command “measure mapStats”; see the following and links therein:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volstats.html>  

Best,
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 Oct 11, 2014, at 1:06 AM, Matthias Fellner <mfellner at chemistry.otago.ac.nz> wrote:

> Dear Elaine
> 
> Thank you for the long response and sorry for my late one as I just finished a publication where I used Chimera for the first time and also cited it. You answered everything I wanted to know.
> 
> So I wanted to wait for my thanks to see if I can ask another question right away:
> What unit do I report for the "level" of a shown electron density map. I assume it is σ (lower case letter sigma) for example 1.2σ?
> 
> I just could not find the unit in the tutorial or a search through your board, so I wanted to double-check.
> 
> Thank you
> Matthias Fellner




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