[chimerax-users] [Chimera-users] convert .mod to .mrc

[Elaine Meng]

Dear Emmanuel Moebel,
I can't think of a simple way to make an index map from IMOD meshes, only a multistep process for each mesh object.  At first I misread the question and thought you said "ChimeraX" so below are steps for both Chimera and ChimeraX in case anybody might be interested.  I have not tried the entire process, however.
I hope this helps,
Elaine

=-=-=
The following instructions are for Chimera:

Each IMOD mesh object from the file is a surface piece.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod.html>

You can specify that surface piece in a "mask" command as "sel" (after selecting it with the mouse) and specifying input map as "ones" to create a map that has values of 1 inside, 0 outside. Then you can scale the map by using "vop scale" to multiply values by a constant (e.g. for values of 2 or 3 instead):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#scale>

Maybe if you did this for multiple mesh objects you could combine the results into one map with "vop add"; not sure how well this would work.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add>

Then you can save your index map as MRC using the Volume Viewer File menu or command "volume"
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization>

=-=-=
The following instructions are for ChimeraX.

Each IMOD mesh object from the file is a surface model in ChimeraX. 
<http://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html>

You can specify that surface model in a "volume onesmask" command to create a map that has values of 1 inside, 0 outside, then multiply values by a constant (e.g. for values of 2 or 3 instead) using "volume scale":
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#scale>

Maybe if you did this for multiple mesh objects you could combine the results into one map with "volume add"; not sure how well this would work.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add>

Then you can use "save" to write your index map as MRC:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 23, 2020, at 7:00 AM, Emmanuel Moebel <emmanuel.moebel at inria.fr> wrote:
> 
> Dear Chimera community,
> 
> I am visualising a tomogram segmentation with Chimera, the format of the file is .mod and has been obtained with the IMOD software. I would like to get a voxel map from it : a volume with integer values, for ex. '0' for background, '1' for membrane, '2' for filament. Output file format needs to be .mrc or .em. Is this possible to achieve with Chimera?
> 
> Thanks in advance,
> Emmanuel Moebel, PhD