[Chimera-users] vop subtract map minRMS
Tom Goddard
goddard at sonic.net
Thu Apr 16 11:40:47 PDT 2020
Hi Roberto,
The f2 value that minimizes the root-mean-square deviation is exactly the difference in mean values between the two maps. But if you are minimizing only within a certain contour level f2 is the difference in mean values within that contour level. Unfortunately I don't know an easy way to get the mean above a contour level. It is too bad the "measure mapStats" does not have that option, it always applies to the whole map. But you could use "measure mapSum" which can sum up the values above the contour level. You would need to mask both maps to the same surface to get means over the same region. And to make it more painful I don't see an easy way to count the grid points in the surface, but you could use the "volume threshold" command to make a map with all ones inside the surface and then mapSum to count the points. This is all perhaps more trouble than it is worth, and it might make sense to fix the offset across the entire map box.
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapSum <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapSum>
Tom
> On Apr 16, 2020, at 8:46 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> 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":
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale>
>
> 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)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapStats>
>
> I hope this helps,
> Elaine
> -----
> 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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