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