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
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