[Chimera-users] Volume planes

[Tom Goddard]

Hi Hernando,

Elaine is right that the displayed step size of the map you are fitting into does not matter -- the fitting will always use the full resolution step 1 data.  The displayed subregion of the map you are fitting into does matter -- the fitting will only use the displayed rectangular subregion. It won't do anything if fitting to a single plane (since it needs to be able to interpolate map values in 3 dimensions so it needs at least 2 planes).  This allows you to limit the region your atomic model will be fit into by cropping the map display.

When fitting one map into another map, both the subregion and the step size for the moving map matter.  The fit will be done using values of the moving map at the grid points within the displayed subregion and using the displayed step size.  You will see if you change the step size of the moving map it will have a usually very small effect on the fit and reported correlation.

I had to look into the code (which I wrote) to be sure of the above rules.  If they are not in the documentation we will try to add them since they are important to understand how to setup a fit calculation.

	Tom



> On Feb 1, 2022, at 8:55 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Hernando,
> 
> (1) there is a setting for what size is shown as a plane.  In Volume Viewer menu, choose Features... Data Display Options. That shows more options in the Volume Viewer dialog.  In those options you can turn off (or change the size) for
> 
> "Show data when opened if smaller than [size] Mvoxels"
> "Show plane when data larger than [size] Mvoxels" 
> 
> See data display options:
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#disp-options>
> 
> Then you can save those settings in your preferences (so they will be used in the future) using Volume Viewer menu "Features... Save default dialog settings"
> 
> (2) for map-map fitting, the "fitmap" command has an "envelope" option of whether to use only the grid points in the fit map with values above the contour level in Volume Viewer. This option is default true but you can set it false to use all nonzero-valued grid points.  See fitmap options:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#options>
> 
> As far as I know, display step size does not affect the calculation.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Jan 31, 2022, at 6:48 PM, Hernando J Sosa via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Dear Chimera,
>> 
>> I have a couple of questions:
>> 	• When open some large volume files with the command open, Chimera by default shows only one plane of the volume. Is there a way to change this default to display all the planes, regardless of volume size?
>> 	• Does the fitmap command results depend on how many planes of the volume are displayed or how it is displayed (e.g. step or level values used)?
>> 
>> Thanks
>> 
>> Hernando
> 
> 
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