[Chimera-users] vop subtract map minRMS

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 16 08:46:19 PDT 2020

Hi Roberto,
(1) yes, the "Level" value for othermap in Volume Viewer is the same as its contour, the value being used to draw its isosurface.  The explanation said "lowest contour value" because you could have more than one isosurface displayed at a time for the same map.

(2) maybe you would want to use a "vop scale" command to subtract the constant (assuming you know what it is) before "vop subtract":

Command "measure mapStats" gives mean, standard deviation (SD) from the mean, and root-mean-square (RMS) deviation from zero for each specified map. (same function as "Volume Mean, SD, RMS" tool in menu)

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 16, 2020, at 6:02 AM, Roberto Marabini <roberto at cnb.csic.es> wrote:
> Hi,
>  I  have two questions regarding the command "vop subtract" with the
> option "minRMS".
> 1st question)
> In the help page the option minRMS is defined as:
> "the min RMS option can be used to scale othermap automatically to
> minimize the root-mean-square sum of the resulting (subtracted) values
> at grid points within the lowest contour of othermap."
> Does this mean that the value that appears in the "Volume viewer"
> window and labeled as "Level" is used to create a contour and all the
> grid pints inside this counter are used to compute the scale factor?
> 2nd question)
> If I understand the command, minRMS assume that the maps (let us
> called them V1 and V2) are related by a multiplicative factor. That is
>     V1 = V2 * f
> where f is a scalar
> In my case
>   V1 = V2 * f1 + f2
> that is, both maps are related by a multiplicative factor (f1) plus
> and additive factor (f2). Is there any chimera command that compute
> the average of a volume so I can force both volume to have the same
> average?
>   Thanks in advance.
>  Roberto

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