Hi Lenka, The IMOD file reader does not handle every kind of annotation that can be put in an IMOD file. That may be why you see nothing. But there are other possibilities like it appears but is not aligned with your other open data in ChimeraX, or other obscure problems, like it opens but is black or fully transparent so you can't see it. At any rate, the IMOD reader is working in current ChimeraX, example image below of some segmentation surfaces read from a .mod format. When ChimeraX read the example .mod file shown below it logged the message Read IMOD model /Users/goddard/ucsf/data/formats/ctl.imod, pixel size 22.55, 5 surfaces which says their were 5 surfaces. Since your message does not say what data was created it probably means the file contained nothing that ChimeraX can handle. Looking at the IMOD reader code (which I wrote long ago) it says it reads surfaces and contours. Tom
On Nov 27, 2024, at 1:50 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Oops, should be "contours true" not "contours false"... although probably "volume mask" is the way to go anyway!
Elaine
On Nov 27, 2024, at 1:45 PM, Elaine Meng via ChimeraX-users <chimerax-users@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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