IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
Dear Sir or Madam, While the 'Input File Types' page <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> 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 Lenka Milojević Biophysics PhD Candidate Z. Hong Zhou Lab University of California, Los Angeles
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
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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: image.png] On Wed, Nov 27, 2024 at 2:42 PM LENKA MILOJEVIC <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> 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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
It's probably what Tom Goddard said, that perhaps the annotations in your file are not the kinds that Chimera(X) interprets as surfaces, or the other possibilities that he listed -- he knows much more about IMOD than I do. <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> Elaine
On Nov 27, 2024, at 2:42 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users@cgl.ucsf.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> 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
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
You cannot, because #1 is not a surface model, according to the error message. It is contours (markers and links). Elaine
On Nov 27, 2024, at 2:46 PM, LENKA MILOJEVIC via ChimeraX-users <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> 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> 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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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> 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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participants (3)
-
Elaine Meng -
LENKA MILOJEVIC -
Tom Goddard