[Chimera-users] How DMIN, DMAX, DMEAN is re-calculated if particular portion of MRC is chopped in Chimera

[SALIM SAZZED]

Dear Mr. Goddard,
Thanks for your quick reply. The script link really helps.


Thanks
Salim Sazzed

On Thu, Apr 13, 2017 at 5:42 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Salim,
>
>   The Chimera MRC file writer puts the minimum, maximum and mean value of
> exactly the grid values that are being written to the MRC file.  So for
> instance if you are writing out a subvolume of a bigger map, the min, max,
> mean are not the values for the bigger map, they are the values for the
> subvolume.  Likewise if you write a subsampled map where only every other
> data value is included along each axis, then only those values are included
> in the min, max, mean.
>
>   Here is the Chimera code that writes MRC:
>
> http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/
> libs/VolumeData/mrc/writemrc.py
>
>   Tom
>
> On Apr 13, 2017, at 11:59 AM, SALIM SAZZED  wrote:
>
> Hello,
> I am a Ph.D. student of Computer Science department at Old Dominion
> University, USA. I am using Chimera for my research. Can you please tell me
> how Chimera calculates *DMIN, DMAX, DMEAN *value of MRC header after
> chopping a portion of original MRC/MAP*?*
>
> My understanding about that-
>
>
> *DMIN: T*he minimum density value of the voxels in the MRC/MAP Cube.
>
> *DMAX: T*he maximum density value of the voxels in the MRC/MAP Cube.
>
> *DMEAN: *The average density of voxels (add all the voxels density value
> and divide it by the number of voxels).
>
>
> It will be really helpful if you clarify.
>
>
> Thanks
> Salim Sazzed
>
>
>
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