Chimera help for tomography data!
Dear All, I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie. I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it? Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated. Thanks and best wishes, Swetha Dr Swetha Vijayakrishnan MRC-University of Glasgow Centre for Virus Research (CVR) University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Garscube campus Glasgow G61 1QH UK Email: Swetha.Vijayakrishnan@glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk> Phone: +44 (0) 141 330 4025 http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/
Hi Sweta, If I understand correctly, you have one volume data set and want to play through its planes. (Volume Series is for when you have multiple 3D data sets.) It sounds like you are using the slider in the Planes section of Volume Viewer to do it manually. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes> To do it automatically, as you would want for a movie script, you can use the “volume” command “planes” option: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes> There is a nice little example at the bottom of this page… you can click the image to see the short movie and then follow the link to see the script that was used: <http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 15, 2017, at 6:19 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan@glasgow.ac.uk> wrote:
Dear All, I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie.
I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it?
Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated. Thanks and best wishes, Swetha
In brief the command to play through volume planes 0-75 looks like volume #0 planes z,0,75 and to record a movie with that you could use movie record ; volume #0 planes z,0,75 ; wait 75 ; movie encode ~/Desktop/planes.mp4 Instead of typing in the command line you can put those commands in a file with suffix “.cmd” and open it, helpful when you add more commands. Tom
On Sep 15, 2017, at 9:19 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Sweta, If I understand correctly, you have one volume data set and want to play through its planes. (Volume Series is for when you have multiple 3D data sets.) It sounds like you are using the slider in the Planes section of Volume Viewer to do it manually. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes>
To do it automatically, as you would want for a movie script, you can use the “volume” command “planes” option: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes>
There is a nice little example at the bottom of this page… you can click the image to see the short movie and then follow the link to see the script that was used: <http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 15, 2017, at 6:19 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan@glasgow.ac.uk> wrote:
Dear All, I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie.
I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it?
Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated. Thanks and best wishes, Swetha
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Thank you Elaine and Tom. That was very useful although i seem to have some trouble encoding the movie. It throws up a Python error that could be a version problem. I shall update to the latest version and check again. The other question i had was how do i fit a model onto the tomogram volume, specifically a 3D structure obtained from subtomogram averaging? Is this possible in the current latest version of chimera? Ideally i would like the planes of the tomogram volume to move through one way and the 3D structure coming up as it moves up the other way. Thanks, Swetha Dr Swetha Vijayakrishnan MRC-University of Glasgow Centre for Virus Research (CVR) University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Garscube campus Glasgow G61 1QH UK Email: Swetha.Vijayakrishnan@glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk> Phone: +44 (0) 141 330 4025 http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/ On 15 Sep 2017, at 18:35, Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> wrote: In brief the command to play through volume planes 0-75 looks like volume #0 planes z,0,75 and to record a movie with that you could use movie record ; volume #0 planes z,0,75 ; wait 75 ; movie encode ~/Desktop/planes.mp4 Instead of typing in the command line you can put those commands in a file with suffix “.cmd” and open it, helpful when you add more commands. Tom On Sep 15, 2017, at 9:19 AM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Sweta, If I understand correctly, you have one volume data set and want to play through its planes. (Volume Series is for when you have multiple 3D data sets.) It sounds like you are using the slider in the Planes section of Volume Viewer to do it manually. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#planes> To do it automatically, as you would want for a movie script, you can use the “volume” command “planes” option: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes> There is a nice little example at the bottom of this page… you can click the image to see the short movie and then follow the link to see the script that was used: <http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 15, 2017, at 6:19 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan@glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk>> wrote: Dear All, I am new to using chimera for EM tomography data. Essentially I am trying to create a movie with tomography and subtomogram data within a single movie. However, i am having trouble making and rendering the movie. I can open the tomogram tilt series (created in IMOD) and manually move it along using the planes option along the axis of interest. However i was trying to see if the Volume series option helps play it automatically but it doesn’t seem to do so. Is this the right way to do it? Any help on how i can play through the tomogram through the various planes back and forth and how i can create a movie will be greatly appreciated. Thanks and best wishes, Swetha _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Swetha, Fitting the structure and then making it appear/disappear using your movie script can be considered two separate issues. You could have the fitted structure saved in a session, so you only do that once. Then you can restore the session and run the movie script, which could include commands to hide/show the model interspersed with planes playback commands. For hide/show, see “modeldisplay” “display” and “ribbon” commands. See command documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> Fitting can be done with the Fit in Map GUI (menu: Tools… Volume Data… Fit in Map) or the “fitmap” command, although the latter includes some additional options not in the GUI, like global search or sequential or symmetrical fitting of multiple subunits. In most cases, the automated fitting is combined with manually (with the mouse) repositioning one model relative to the other. Once the fit is to your liking, then save the session for use with your movie script. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> Moving models by hand: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> We wouldn’t be able to comment on the recording error unless you provide more details. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2017, at 3:14 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan@glasgow.ac.uk> wrote:
Thank you Elaine and Tom. That was very useful although i seem to have some trouble encoding the movie. It throws up a Python error that could be a version problem. I shall update to the latest version and check again.
The other question i had was how do i fit a model onto the tomogram volume, specifically a 3D structure obtained from subtomogram averaging? Is this possible in the current latest version of chimera? Ideally i would like the planes of the tomogram volume to move through one way and the 3D structure coming up as it moves up the other way.
Thanks, Swetha
Hi Elaine, Thanks for this input. I did manage to fit the models into the tomogram and use the model display as well. However i was trying to clip some of the fit structural models to show the interior which at the moment i am struggling with using clip or the mclip options. Any advice on this from you will be greatly appreciated. Also i was trying to save the chimera session to get back to another time, but i seem to be getting an error msg saying one of the volumes has not been saved, i.e. the original tomogram that was rescaled and inverted using the volume filter/scale options and that appears as a new model now in my volume viewer. I tried using the "save map” option selecting this model and naming it as .mrc in the volume viewer menu prior to resaving the session but i am still unable to do so and keep getting the same error (see attached below). How do i solve this problem? Thanks and Best, Swetha [cid:FB049C5C-AD56-4384-BC8F-5CB6CC23A586@campus.gla.ac.uk] Dr Swetha Vijayakrishnan MRC-University of Glasgow Centre for Virus Research (CVR) University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Garscube campus Glasgow G61 1QH UK Email: Swetha.Vijayakrishnan@glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk> Phone: +44 (0) 141 330 4025 http://www.gla.ac.uk/colleges/mvls/supportforresearch/nerd/ On 20 Sep 2017, at 17:36, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Swetha, Fitting the structure and then making it appear/disappear using your movie script can be considered two separate issues. You could have the fitted structure saved in a session, so you only do that once. Then you can restore the session and run the movie script, which could include commands to hide/show the model interspersed with planes playback commands. For hide/show, see “modeldisplay” “display” and “ribbon” commands. See command documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> Fitting can be done with the Fit in Map GUI (menu: Tools… Volume Data… Fit in Map) or the “fitmap” command, although the latter includes some additional options not in the GUI, like global search or sequential or symmetrical fitting of multiple subunits. In most cases, the automated fitting is combined with manually (with the mouse) repositioning one model relative to the other. Once the fit is to your liking, then save the session for use with your movie script. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> Moving models by hand: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> We wouldn’t be able to comment on the recording error unless you provide more details. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 20, 2017, at 3:14 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan@glasgow.ac.uk<mailto:Swetha.Vijayakrishnan@glasgow.ac.uk>> wrote: Thank you Elaine and Tom. That was very useful although i seem to have some trouble encoding the movie. It throws up a Python error that could be a version problem. I shall update to the latest version and check again. The other question i had was how do i fit a model onto the tomogram volume, specifically a 3D structure obtained from subtomogram averaging? Is this possible in the current latest version of chimera? Ideally i would like the planes of the tomogram volume to move through one way and the 3D structure coming up as it moves up the other way. Thanks, Swetha
Hi Swetha, Maybe you had trouble saving the right one if you had several map models with similar names. First choose that map’s name from the Volume Viewer “Data” menu to make sure it is shown in the dialog and is the active one. Then use Volume Viewer menu: File… Save Map As… to save it to a file (or if you know the model number of that map, you could also use the “volume” command to save it, e.g. “volume #3 save ~/Desktop/mymap.mrc” ) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> I have no idea what problems you are having with clipping. Maybe command syntax? “clip” is for clipping everything at the same time, “mclip” is for if you want to clip some model(s) but not others. If you are OK with clipping everything at the same time it will be easier to do it interactively with the Side View (main menu: Favorites… Side View) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2017, at 8:35 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan@glasgow.ac.uk> wrote:
Hi Elaine, Thanks for this input. I did manage to fit the models into the tomogram and use the model display as well.
However i was trying to clip some of the fit structural models to show the interior which at the moment i am struggling with using clip or the mclip options. Any advice on this from you will be greatly appreciated.
Also i was trying to save the chimera session to get back to another time, but i seem to be getting an error msg saying one of the volumes has not been saved, i.e. the original tomogram that was rescaled and inverted using the volume filter/scale options and that appears as a new model now in my volume viewer. I tried using the "save map” option selecting this model and naming it as .mrc in the volume viewer menu prior to resaving the session but i am still unable to do so and keep getting the same error (see attached below). How do i solve this problem?
Thanks and Best, Swetha
Hi Swetha, I’d forgotten you were working on scripting a movie, and so you would need to use commands to clip instead of the interactive Side View. In that case, see the clipping/slicing script examples in the bottom section of this page: <http://www.rbvi.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> … and there is another example in the Animation Gallery, "Bacteriophage phi6” about half of the way down the page. <http://www.rbvi.ucsf.edu/chimera/animations/animations.html> Best, Elaine
On Oct 5, 2017, at 10:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Swetha, Maybe you had trouble saving the right one if you had several map models with similar names. First choose that map’s name from the Volume Viewer “Data” menu to make sure it is shown in the dialog and is the active one. Then use Volume Viewer menu: File… Save Map As… to save it to a file (or if you know the model number of that map, you could also use the “volume” command to save it, e.g. “volume #3 save ~/Desktop/mymap.mrc” ) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>
I have no idea what problems you are having with clipping. Maybe command syntax? “clip” is for clipping everything at the same time, “mclip” is for if you want to clip some model(s) but not others. If you are OK with clipping everything at the same time it will be easier to do it interactively with the Side View (main menu: Favorites… Side View) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2017, at 8:35 AM, Swetha Vijayakrishnan <Swetha.Vijayakrishnan@glasgow.ac.uk> wrote:
Hi Elaine, Thanks for this input. I did manage to fit the models into the tomogram and use the model display as well.
However i was trying to clip some of the fit structural models to show the interior which at the moment i am struggling with using clip or the mclip options. Any advice on this from you will be greatly appreciated.
Also i was trying to save the chimera session to get back to another time, but i seem to be getting an error msg saying one of the volumes has not been saved, i.e. the original tomogram that was rescaled and inverted using the volume filter/scale options and that appears as a new model now in my volume viewer. I tried using the "save map” option selecting this model and naming it as .mrc in the volume viewer menu prior to resaving the session but i am still unable to do so and keep getting the same error (see attached below). How do i solve this problem?
Thanks and Best, Swetha
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participants (3)
-
Elaine Meng -
Swetha Vijayakrishnan -
Tom Goddard