[chimerax-users] Regarding generating volume surface in ChimeraX for large maps

[Tom Goddard]

Hi Rakesh,

  ChimeraX displays just a single plane when you open a map file larger than 256 Mvoxels -- often the situation for electron microscopy tomograms, for example a 2048 by 2048 by 100 map (400 Mvoxels), but also for large electron microscopy single particle reconstructions, e.g. 800 x 800 x 800 (512 Mvoxels).  Maps larger than 16 Mvoxels will not be shown at full resolution (step 1), instead the step size will be chosen to only display at most 16 Mvoxels when the map is first opened, again to improve load speed for common interactive use cases.

  So if you are writing a script and need the full map shown always include a volume command to assure it is shown how you want, for example to show all planes,

	volume #1 region all style surface

or to assure it is shown at full resolution

	volume #1 step 1 region all style surface

and to make sure the threshold level is what you want you can specify it too

	volume #1 level 4.5 step 1 region all style surface

There are volume command options that set the 256 MVoxel limit for planes (option name "voxelLimitForPlane") and 16 MVoxel full resolution limit (option name "voxelLimit") that you can use to change the default for the current session, but unfortunately ChimeraX currently does not offer a way to save new default values.

  These are all documented

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling

  Tom


> On Feb 18, 2022, at 12:47 PM, Rakesh Ramachandran <rakeshramachandran10 at gmail.com> wrote:
> 
> Hi Tom,
> 
>    I am trying to segment volume using 'volume splitbyzone' in ChimeraX for a large number of maps. But what I observed is that some of the maps are displayed as planes instead of surfaces and this affects the volume splitbyzone command. 
> 
>   I tried using 'volume style surface' but it doesn't seem to work unless I manually set it in the GUI. What option do I use to generate surfaces for map volumes automatically from the command line in such cases?
> 
> -- 
> Regards
> Rakesh Ramachandran
> Postdoctoral Scholar
> Department of Bioengineering and Therapeutic Sciences
> University of California, San Francisco
> Byers Hall Room 501
> 1700 4th Street
> San Francisco, CA  94143, USA