Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large.
Cheers
MGM
Martin G Montgomery Senior Scientist ATP Synthase Group MRC Mitochondrial Biology Unit University of Cambridge The Keith Peters Building Cambridge Biomedical Campus Hills Road Cambridge Great Britain CB2 0XY
www.mrc-mbu.cam.ac.uk http://www.mrc-mbu.cam.ac.uk/
Hi Martin, Yes, in ChimeraX the way to do this is with named views. You can have several different named views in a single session file. We do not have saveable "scenes" (changes in display, color etc.) yet, just the positioning part, the views. So if there were lots of display changes between your figures it would be better to save separate sessions. If the main difference between figures is positioning (or very simple display changes like hiding one model), then you could consider saving multiple views in the same session file.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session
Another thing you may be interested in is reporting and applying matrices, but to me that just seems like a more difficult way to accomplish the same thing as using named views.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix
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 20, 2020, at 12:41 AM, Martin Montgomery mgm@mrc-mbu.cam.ac.uk wrote:
Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM
Not sure how my previous reply went to ChimeraX-bugs - sorry about that!
One good reason for using "view matrix" and applying a script to regenerate the scene rather than simply saving a session is that for experimentalists the model itself might change - that is, the figure is made, then an error is picked up in the model and it's re-refined, so the figure needs to be regenerated from a new file.
On 2020-05-21 17:51, Elaine Meng wrote:
Hi Martin, Yes, in ChimeraX the way to do this is with named views. You can have several different named views in a single session file. We do not have saveable "scenes" (changes in display, color etc.) yet, just the positioning part, the views. So if there were lots of display changes between your figures it would be better to save separate sessions. If the main difference between figures is positioning (or very simple display changes like hiding one model), then you could consider saving multiple views in the same session file.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session
Another thing you may be interested in is reporting and applying matrices, but to me that just seems like a more difficult way to accomplish the same thing as using named views.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix
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 20, 2020, at 12:41 AM, Martin Montgomery mgm@mrc-mbu.cam.ac.uk wrote:
Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tristan,
It gets really hard to restore all the settings used to make a figure using commands like "view matrix" and "camera" to find field of view, and trying to match the colors and styles and lighting.... A better approach is always save a ChimeraX session used to make the figure, I usually give it the same file name as the figure image file. Then when the model is revised, open the original session, load the new model, color and style it the same as the old, close the old model, and save the revised figure session. It is also useful to use "view name figure" to name the camera view and model positions used for the image so you can rotate the view around and still easily get back to the figure view point with "view figure". The named views are saved in sessions.
Tom
On May 21, 2020, at 10:05 AM, Tristan Croll tic20@cam.ac.uk wrote:
Not sure how my previous reply went to ChimeraX-bugs - sorry about that!
One good reason for using "view matrix" and applying a script to regenerate the scene rather than simply saving a session is that for experimentalists the model itself might change - that is, the figure is made, then an error is picked up in the model and it's re-refined, so the figure needs to be regenerated from a new file.
On 2020-05-21 17:51, Elaine Meng wrote:
Hi Martin, Yes, in ChimeraX the way to do this is with named views. You can have several different named views in a single session file. We do not have saveable "scenes" (changes in display, color etc.) yet, just the positioning part, the views. So if there were lots of display changes between your figures it would be better to save separate sessions. If the main difference between figures is positioning (or very simple display changes like hiding one model), then you could consider saving multiple views in the same session file. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session Another thing you may be interested in is reporting and applying matrices, but to me that just seems like a more difficult way to accomplish the same thing as using named views. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix 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 20, 2020, at 12:41 AM, Martin Montgomery mgm@mrc-mbu.cam.ac.uk wrote: Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom - for coloring it the same as the old - is there an equivalent of the “mcopy” command in chimeraX yet? Absent support for scenes that would be the next best thing
Cheers Oli
On May 21, 2020 at 17:15 GMT, Tom Goddard goddard@sonic.net wrote:
Hi Tristan,
It gets really hard to restore all the settings used to make a figure using commands like "view matrix" and "camera" to find field of view, and trying to match the colors and styles and lighting.... A better approach is always save a ChimeraX session used to make the figure, I usually give it the same file name as the figure image file. Then when the model is revised, open the original session, load the new model, color and style it the same as the old, close the old model, and save the revised figure session. It is also useful to use "view name figure" to name the camera view and model positions used for the image so you can rotate the view around and still easily get back to the figure view point with "view figure". The named views are saved in sessions.
Tom
On May 21, 2020, at 10:05 AM, Tristan Croll tic20@cam.ac.uk wrote:
Not sure how my previous reply went to ChimeraX-bugs - sorry about that!
One good reason for using "view matrix" and applying a script to regenerate the scene rather than simply saving a session is that for experimentalists the model itself might change - that is, the figure is made, then an error is picked up in the model and it's re-refined, so the figure needs to be regenerated from a new file.
On 2020-05-21 17:51, Elaine Meng wrote:
Hi Martin, Yes, in ChimeraX the way to do this is with named views. You can have several different named views in a single session file. We do not have saveable "scenes" (changes in display, color etc.) yet, just the positioning part, the views. So if there were lots of display changes between your figures it would be better to save separate sessions. If the main difference between figures is positioning (or very simple display changes like hiding one model), then you could consider saving multiple views in the same session file. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session Another thing you may be interested in is reporting and applying matrices, but to me that just seems like a more difficult way to accomplish the same thing as using named views. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix 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 20, 2020, at 12:41 AM, Martin Montgomery mgm@mrc-mbu.cam.ac.uk wrote: Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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We don't have mcopy to copy molecule settings in ChimeraX yet -- I agree that would be handy.
https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mcopy.html
Tom
On May 21, 2020, at 10:18 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi Tom - for coloring it the same as the old - is there an equivalent of the “mcopy” command in chimeraX yet? Absent support for scenes that would be the next best thing
Cheers Oli
On May 21, 2020 at 17:15 GMT, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Tristan,
It gets really hard to restore all the settings used to make a figure using commands like "view matrix" and "camera" to find field of view, and trying to match the colors and styles and lighting.... A better approach is always save a ChimeraX session used to make the figure, I usually give it the same file name as the figure image file. Then when the model is revised, open the original session, load the new model, color and style it the same as the old, close the old model, and save the revised figure session. It is also useful to use "view name figure" to name the camera view and model positions used for the image so you can rotate the view around and still easily get back to the figure view point with "view figure". The named views are saved in sessions.
Tom
On May 21, 2020, at 10:05 AM, Tristan Croll <tic20@cam.ac.uk mailto:tic20@cam.ac.uk> wrote:
Not sure how my previous reply went to ChimeraX-bugs - sorry about that!
One good reason for using "view matrix" and applying a script to regenerate the scene rather than simply saving a session is that for experimentalists the model itself might change - that is, the figure is made, then an error is picked up in the model and it's re-refined, so the figure needs to be regenerated from a new file.
On 2020-05-21 17:51, Elaine Meng wrote:
Hi Martin, Yes, in ChimeraX the way to do this is with named views. You can have several different named views in a single session file. We do not have saveable "scenes" (changes in display, color etc.) yet, just the positioning part, the views. So if there were lots of display changes between your figures it would be better to save separate sessions. If the main difference between figures is positioning (or very simple display changes like hiding one model), then you could consider saving multiple views in the same session file. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> Another thing you may be interested in is reporting and applying matrices, but to me that just seems like a more difficult way to accomplish the same thing as using named views. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> 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 20, 2020, at 12:41 AM, Martin Montgomery <mgm@mrc-mbu.cam.ac.uk mailto:mgm@mrc-mbu.cam.ac.uk> wrote: Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Thanks for the info and discussion, Everyone. Very useful.
Cheers
MGM
On 21 May 2020, at 18:05, Tristan Croll tic20@CAM.AC.UK wrote:
Not sure how my previous reply went to ChimeraX-bugs - sorry about that!
One good reason for using "view matrix" and applying a script to regenerate the scene rather than simply saving a session is that for experimentalists the model itself might change - that is, the figure is made, then an error is picked up in the model and it's re-refined, so the figure needs to be regenerated from a new file.
On 2020-05-21 17:51, Elaine Meng wrote:
Hi Martin, Yes, in ChimeraX the way to do this is with named views. You can have several different named views in a single session file. We do not have saveable "scenes" (changes in display, color etc.) yet, just the positioning part, the views. So if there were lots of display changes between your figures it would be better to save separate sessions. If the main difference between figures is positioning (or very simple display changes like hiding one model), then you could consider saving multiple views in the same session file. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session Another thing you may be interested in is reporting and applying matrices, but to me that just seems like a more difficult way to accomplish the same thing as using named views. http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix 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 20, 2020, at 12:41 AM, Martin Montgomery mgm@mrc-mbu.cam.ac.uk wrote: Hi, I have a session file that contains everything I need to make figures for a paper. With pymol, I saved the get_view matrix in a text file for each view which meant that with one session file I could easily recreate the views if I needed to go back and tweak a figure. In ChimeraX, the closest way that I found to replicate this was to use named views. Am happy to supply a session file if it helps also happy to be educated if there is a better way of doing this, especially as now the ChimeraX session files can get rather large. Cheers MGM
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (5)
-
Elaine Meng -
Martin Montgomery -
Oliver Clarke -
Tom Goddard -
Tristan Croll