[Chimera-users] Volume planes

[Elaine Meng]

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