Hi Elaine, 

If I don't input contours true, nothing shows up on my screen. It just states it read it.

open C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod

Read IMOD model C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod, pixel size 0.568

Sorry for the trouble. I really appreciate your help.

Best,

Lenka

On Wed, Nov 27, 2024 at 2:09 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Lenka,
Contours true is to make it into markers and links (fake atoms and bonds) instead of a surface.  You do not need markers and links for masking, you only need a surface model (meshes true contours false).

Just open the file directly without any options and by default it should make a surface model that you can use in "volume mask"  - I thought "meshes true" would still make the surface but maybe it only does that when contours is false.

I'm sorry I mentioned the contours option since it was confusing... I only did so because at first I thought you wanted markers.

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

> On Nov 27, 2024, at 1:34 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear Dr. Meng,
>
> Thank you! I've now managed to open the segmentation with open C:Path format imod meshes true contours true. But If I run volume mask it just outputs:
> volume mask #3 surfaces #1 fullMap true
> No surfaces specified
> volume mask #3 #1 extend 3
> Missing required "surfaces" argument
> volume mask #3 surfaces #1
> No surfaces specified
>
> Any advice? Is the contour not actually a surface yet? Or am I writing the command wrong.
>
> Thank you so so much!
>
> Best,
> Lenka
>
> On Wed, Nov 27, 2024 at 1:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
> Hi Lenka,
> The link that you sent is to the Chimera documentation (not ChimeraX):
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object>
>
> Since they are different programs, there are differences... but not in this case!  ChimeraX can also open these IMOD segmentations:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation>
> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html>
>
> These segmentation models are surfaces, not the atoms or pseudoatoms (markers) that you would need to define a zone with Color Zone.   Although the second link above explains that you can make the IMOD surface mesh into markers/links by opening the file with  the "open" command option "contours false," that is unlikely to make them suitable for defining zones.  Mainly it is used to improve display.
>
> Instead you can use "volume mask" to mask parts of your map with the IMOD segmentation surfaces.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Resource for Biocomputing, Visualization, and Informatics
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 27, 2024, at 11:56 AM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
> >
> > Dear Sir or Madam,
> >
> > While the 'Input File Types' page lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'.
> >
> > I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD.
> >
> > I appreciate your time and assistance!
> >
> > Sincerely,
> > Lenka
>
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