Making movie of whole cell model with EM images
Hello, My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you! -- George A. Schaible, Ph.D Dept. of Chemistry & Biochemistry Montana State University Google Scholar profile <https://scholar.google.com/citations?user=_M2xvYIAAAAJ&hl=en>
Hi George, The first thing to do is see if you can open and display your data files in ChimeraX. I don't know what formats you have for your EM map or your model. ChimeraX can read lots of map formats: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> As for your model, is it written out from IMOD? ChimeraX can read IMOD segmentations <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> Assuming you can read and display the data as you like, then the next thing is what you want in your movie. Do you just want it to rotate about the vertical axis once, or do you aspire to more complicated motions with multiple rotations and zooms, and/or playing through planes of the data or showing a sliding slab? If it's just to rotate it around once, you could even try just clicking the movie-recorder icon in the top bar, which will automatically do that and save a movie file. If you want the other fancier stuff, you would make a text file containing a series of ChimeraX commands and then open it to execute the commands. Command files: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...> Various movie-relevant ChimeraX commands are listed on our "making movies" page, along with links to example movie scripts. <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> For playing through the planes of data or showing a sliding slab, see also the "volume" command planes options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#planes> Normally you would enter these commands interactively in the command line to try them out before even bothering to put them in your ChimeraX command file. Even after you start making a command file it is normally an iterative process of adding and modifying commands until the potential movie content satisfies you. Then finally as the last step you would bracket the other commands in the file with ones to start recording the movie and then at the end encode it into a movie file ("movie" command). Typically you would also save a session with your data displayed how you like it, so that in the future to reproduce the movie you would simply need to reopen the session and then open your previously written movie command script. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2024, at 11:29 AM, George Schaible via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you!
Thank you Elaine, this is all very helpful!! I can load in my model no problem and I have some experience making simple density movies in ChimeraX but the links you shared will greatly improve my ability to make the final product. My goal is to make a movie similar to the one that Ricardo Righetto shared with me: https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-04971-z/M... The biggest issue I am having currently is opening the .mrc file of the SBF-EM data with the model in ChimeraX, then aligning the two and making the movie. I wasn't sure if there were any tutorials on this and if not, I might have some folks I can talk to on campus that can help. Thank you so much for your very detailed response! On Mon, May 6, 2024 at 1:14 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, The first thing to do is see if you can open and display your data files in ChimeraX. I don't know what formats you have for your EM map or your model. ChimeraX can read lots of map formats: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
As for your model, is it written out from IMOD? ChimeraX can read IMOD segmentations <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html>
Assuming you can read and display the data as you like, then the next thing is what you want in your movie. Do you just want it to rotate about the vertical axis once, or do you aspire to more complicated motions with multiple rotations and zooms, and/or playing through planes of the data or showing a sliding slab?
If it's just to rotate it around once, you could even try just clicking the movie-recorder icon in the top bar, which will automatically do that and save a movie file.
If you want the other fancier stuff, you would make a text file containing a series of ChimeraX commands and then open it to execute the commands. Command files: < https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...
Various movie-relevant ChimeraX commands are listed on our "making movies" page, along with links to example movie scripts. <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
For playing through the planes of data or showing a sliding slab, see also the "volume" command planes options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#planes>
Normally you would enter these commands interactively in the command line to try them out before even bothering to put them in your ChimeraX command file. Even after you start making a command file it is normally an iterative process of adding and modifying commands until the potential movie content satisfies you. Then finally as the last step you would bracket the other commands in the file with ones to start recording the movie and then at the end encode it into a movie file ("movie" command). Typically you would also save a session with your data displayed how you like it, so that in the future to reproduce the movie you would simply need to reopen the session and then open your previously written movie command script.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2024, at 11:29 AM, George Schaible via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you!
-- George A. Schaible, Ph.D Dept. of Chemistry & Biochemistry Montana State University Google Scholar profile <https://scholar.google.com/citations?user=_M2xvYIAAAAJ&hl=en>
Hi George, If he made the movie with ChimeraX, maybe Ricardo Righetto would be willing to share with you (privately) his command script? If your segmentation surfaces (I guess that is what you mean by model) and data are not automatically in register with one another, as far as I know you would need to move one relative to the other "manually" ... in the case of using the mouse to move only some models instead of the whole scene, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> You can also use "move" (translate) and "turn" (rotate) commands with their "models" option to move only the specified models instead of the whole scene, if you need to do some precise amounts that are difficult with the mouse/touchpad. Then after the two are in the proper register, if there are different views of the whole scene (e.g. from different angles or zoomed in) you want to include in your movie, you can generate them by moving the system around by hand and then saving each view in turn with "view name" before saving the session. In Ricardo's movie, it looks like he might be using "view" to transition between such previously saved views and maybe "crossfade" to fade some parts between hidden/shown states. You would need the different surfaces to be in different model or submodel numbers in order to specify them separately in show/hide commands. The move, turn, and view commands are included in list of commands commonly used in movie-making, and of course you can use other commands as needed (hide, show, color, ...) <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> <https://rbvi.ucsf.edu/chimerax/docs/user/images.html> 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 May 7, 2024, at 7:58 AM, George Schaible via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine, this is all very helpful!! I can load in my model no problem and I have some experience making simple density movies in ChimeraX but the links you shared will greatly improve my ability to make the final product.
My goal is to make a movie similar to the one that Ricardo Righetto shared with me: https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-04971-z/M...
The biggest issue I am having currently is opening the .mrc file of the SBF-EM data with the model in ChimeraX, then aligning the two and making the movie. I wasn't sure if there were any tutorials on this and if not, I might have some folks I can talk to on campus that can help. Thank you so much for your very detailed response!
On Mon, May 6, 2024 at 1:14 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi George, The first thing to do is see if you can open and display your data files in ChimeraX. I don't know what formats you have for your EM map or your model. ChimeraX can read lots of map formats: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
As for your model, is it written out from IMOD? ChimeraX can read IMOD segmentations <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html>
Assuming you can read and display the data as you like, then the next thing is what you want in your movie. Do you just want it to rotate about the vertical axis once, or do you aspire to more complicated motions with multiple rotations and zooms, and/or playing through planes of the data or showing a sliding slab?
If it's just to rotate it around once, you could even try just clicking the movie-recorder icon in the top bar, which will automatically do that and save a movie file.
If you want the other fancier stuff, you would make a text file containing a series of ChimeraX commands and then open it to execute the commands. Command files: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...>
Various movie-relevant ChimeraX commands are listed on our "making movies" page, along with links to example movie scripts. <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
For playing through the planes of data or showing a sliding slab, see also the "volume" command planes options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#planes>
Normally you would enter these commands interactively in the command line to try them out before even bothering to put them in your ChimeraX command file. Even after you start making a command file it is normally an iterative process of adding and modifying commands until the potential movie content satisfies you. Then finally as the last step you would bracket the other commands in the file with ones to start recording the movie and then at the end encode it into a movie file ("movie" command). Typically you would also save a session with your data displayed how you like it, so that in the future to reproduce the movie you would simply need to reopen the session and then open your previously written movie command script.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2024, at 11:29 AM, George Schaible via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you!
Hi Elaine, hi George, For completeness, I attach here the scripts that I used to make the movie sent by George in ChimeraX. Indeed, I make use of named views to transition between different things I want to show, together with the 'crossfade' and 'perframe' commands (among others) where applicable. As Elaine suggested, it takes some trial and error to achieve the desired result. What I found tricky at the time I made this movie was to understand that I had to use the 'wait' command with enough frames to ensure the previous action would complete before moving on to the next command. Best wishes, -- Ricardo Diogo Righetto Em ter., 7 de mai. de 2024 às 18:27, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> escreveu:
Hi George, If he made the movie with ChimeraX, maybe Ricardo Righetto would be willing to share with you (privately) his command script?
If your segmentation surfaces (I guess that is what you mean by model) and data are not automatically in register with one another, as far as I know you would need to move one relative to the other "manually" ... in the case of using the mouse to move only some models instead of the whole scene, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective>
You can also use "move" (translate) and "turn" (rotate) commands with their "models" option to move only the specified models instead of the whole scene, if you need to do some precise amounts that are difficult with the mouse/touchpad.
Then after the two are in the proper register, if there are different views of the whole scene (e.g. from different angles or zoomed in) you want to include in your movie, you can generate them by moving the system around by hand and then saving each view in turn with "view name" before saving the session.
In Ricardo's movie, it looks like he might be using "view" to transition between such previously saved views and maybe "crossfade" to fade some parts between hidden/shown states. You would need the different surfaces to be in different model or submodel numbers in order to specify them separately in show/hide commands.
The move, turn, and view commands are included in list of commands commonly used in movie-making, and of course you can use other commands as needed (hide, show, color, ...) <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> <https://rbvi.ucsf.edu/chimerax/docs/user/images.html>
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 May 7, 2024, at 7:58 AM, George Schaible via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine, this is all very helpful!! I can load in my model no problem and I have some experience making simple density movies in ChimeraX but the links you shared will greatly improve my ability to make the final product.
My goal is to make a movie similar to the one that Ricardo Righetto shared with me:
https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-04971-z/M...
The biggest issue I am having currently is opening the .mrc file of the
SBF-EM data with the model in ChimeraX, then aligning the two and making the movie. I wasn't sure if there were any tutorials on this and if not, I might have some folks I can talk to on campus that can help. Thank you so much for your very detailed response!
On Mon, May 6, 2024 at 1:14 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi George, The first thing to do is see if you can open and display your data files
in ChimeraX. I don't know what formats you have for your EM map or your model. ChimeraX can read lots of map formats:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
As for your model, is it written out from IMOD? ChimeraX can read IMOD segmentations < https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html>
Assuming you can read and display the data as you like, then the next thing is what you want in your movie. Do you just want it to rotate about the vertical axis once, or do you aspire to more complicated motions with multiple rotations and zooms, and/or playing through planes of the data or showing a sliding slab?
If it's just to rotate it around once, you could even try just clicking the movie-recorder icon in the top bar, which will automatically do that and save a movie file.
If you want the other fancier stuff, you would make a text file containing a series of ChimeraX commands and then open it to execute the commands. Command files: < https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...
Various movie-relevant ChimeraX commands are listed on our "making movies" page, along with links to example movie scripts. <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
For playing through the planes of data or showing a sliding slab, see also the "volume" command planes options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#planes>
Normally you would enter these commands interactively in the command line to try them out before even bothering to put them in your ChimeraX command file. Even after you start making a command file it is normally an iterative process of adding and modifying commands until the potential movie content satisfies you. Then finally as the last step you would bracket the other commands in the file with ones to start recording the movie and then at the end encode it into a movie file ("movie" command). Typically you would also save a session with your data displayed how you like it, so that in the future to reproduce the movie you would simply need to reopen the session and then open your previously written movie command script.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2024, at 11:29 AM, George Schaible via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you!
_______________________________________________ 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 George, If your IMOD model and serial block face MRC map do not align correctly then it may be a problem with IMOD ignoring the map origin while ChimeraX uses it. By changing the map origin to 0 you may fix this. Use ChimeraX menu Tools / Volume Data / Map Coordinates to see what the map origin is (as read from the MRC file) and change it. I don't recommend trying to realign by hand -- there is no way you will get it exactly right by hand. Tom
On May 7, 2024, at 9:25 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi George, If he made the movie with ChimeraX, maybe Ricardo Righetto would be willing to share with you (privately) his command script?
If your segmentation surfaces (I guess that is what you mean by model) and data are not automatically in register with one another, as far as I know you would need to move one relative to the other "manually" ... in the case of using the mouse to move only some models instead of the whole scene, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective>
You can also use "move" (translate) and "turn" (rotate) commands with their "models" option to move only the specified models instead of the whole scene, if you need to do some precise amounts that are difficult with the mouse/touchpad.
Then after the two are in the proper register, if there are different views of the whole scene (e.g. from different angles or zoomed in) you want to include in your movie, you can generate them by moving the system around by hand and then saving each view in turn with "view name" before saving the session.
In Ricardo's movie, it looks like he might be using "view" to transition between such previously saved views and maybe "crossfade" to fade some parts between hidden/shown states. You would need the different surfaces to be in different model or submodel numbers in order to specify them separately in show/hide commands.
The move, turn, and view commands are included in list of commands commonly used in movie-making, and of course you can use other commands as needed (hide, show, color, ...) <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> <https://rbvi.ucsf.edu/chimerax/docs/user/images.html>
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 May 7, 2024, at 7:58 AM, George Schaible via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine, this is all very helpful!! I can load in my model no problem and I have some experience making simple density movies in ChimeraX but the links you shared will greatly improve my ability to make the final product.
My goal is to make a movie similar to the one that Ricardo Righetto shared with me: https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-04971-z/M...
The biggest issue I am having currently is opening the .mrc file of the SBF-EM data with the model in ChimeraX, then aligning the two and making the movie. I wasn't sure if there were any tutorials on this and if not, I might have some folks I can talk to on campus that can help. Thank you so much for your very detailed response!
On Mon, May 6, 2024 at 1:14 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi George, The first thing to do is see if you can open and display your data files in ChimeraX. I don't know what formats you have for your EM map or your model. ChimeraX can read lots of map formats: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume>
As for your model, is it written out from IMOD? ChimeraX can read IMOD segmentations <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html>
Assuming you can read and display the data as you like, then the next thing is what you want in your movie. Do you just want it to rotate about the vertical axis once, or do you aspire to more complicated motions with multiple rotations and zooms, and/or playing through planes of the data or showing a sliding slab?
If it's just to rotate it around once, you could even try just clicking the movie-recorder icon in the top bar, which will automatically do that and save a movie file.
If you want the other fancier stuff, you would make a text file containing a series of ChimeraX commands and then open it to execute the commands. Command files: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...>
Various movie-relevant ChimeraX commands are listed on our "making movies" page, along with links to example movie scripts. <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html>
For playing through the planes of data or showing a sliding slab, see also the "volume" command planes options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#planes>
Normally you would enter these commands interactively in the command line to try them out before even bothering to put them in your ChimeraX command file. Even after you start making a command file it is normally an iterative process of adding and modifying commands until the potential movie content satisfies you. Then finally as the last step you would bracket the other commands in the file with ones to start recording the movie and then at the end encode it into a movie file ("movie" command). Typically you would also save a session with your data displayed how you like it, so that in the future to reproduce the movie you would simply need to reopen the session and then open your previously written movie command script.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 6, 2024, at 11:29 AM, George Schaible via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you!
_______________________________________________ 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/
participants (4)
-
Elaine Meng -
George Schaible -
Ricardo Righetto -
Tom Goddard