Re: IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
Glad you got it to work. Tom
On Nov 27, 2024, at 3:30 PM, LENKA MILOJEVIC <lenka11@g.ucla.edu> wrote:
Dear Dr. Goddard,
Thank you so much! That worked! I thought I’d have to produce a .cmm file or mask the map using the volume tool and the .mod file as a surface.
I really appreciate your swift responses! This was incredibly helpful.
Have a great rest of your day!
Sincerely, Lenka
On Wed, 27 Nov 2024 at 15:26, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Lenka,
Seems like you got what you wanted "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." Your image shows the traced curves as connected markers (fake atoms connected by bonds). To color the nearby density you would then use the Color Zone tool, menu Tools / Volume Data / Color Zone and it has a Split Map button that would let you make a new map that includes just the colored part near your curves. The equivalent ChimeraX command is "color zone"
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone
If the command syntax is confusing just use the graphical Color Zone tool and it will log the equivalent command to the Log panel and you will have a better idea of how to type a command if you want to use some of the fancier options (like bondPointSpacing) that the graphical tool does not offer.
Tom
On Nov 27, 2024, at 2:46 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
In the event that I want to mask map #3 using the .mod file in #1 , which command exactly do I run? I'm attaching a screenshot showing my current session. <image.png>
On Wed, Nov 27, 2024 at 2:42 PM LENKA MILOJEVIC <lenka11@g.ucla.edu <mailto:lenka11@g.ucla.edu>> wrote:
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 <mailto: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 <mailto: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 <mailto: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 <mailto: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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Tom Goddard