Hi Vincent, I always save a session file with the view for each publication image. Trying to do it this other way is much harder, in my opinion, and I have never tried it myself. As far as I know, the "view matrix" command should report (and restore) the camera and model positions, and "clip list" report (and "clip" restore) the clipping plane position(s): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html> What you showed for results from "clip list" does not make sense: the near and far planes do not have a tilt axis, so their axis will only be 0,0,1 or 0,0,-1. But you said "modified" so maybe you edited it? It is impossible for me to tell what is really in your session if you don't include the whole results for clip list. Then if you want it to look the same you should set exactly the same clip plane(s) as reported by clip list. If you have a front or back plane, you should also set the reported axis ("axis" option of "clip", see help above) and point cordinates ("position" option of "clip"). If it is not working and you feel it is a bug, please use Help... Report a Bug and attach the session, and the details of how you tried to reproduce it; however, that would put your data in a publicly available repository. If you have a simpler example you could attach that to the bug report instead. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 28, 2023, at 7:48 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I've been playing around with it but I can't get to what I want. The second option of saving views works within a session, but it is lost if I restart ChimeraX or changes session, so what I'm looking for is really some numbers to place in a script so I can touch up my figure for publication multiple times.
Using "clip list" does list me an offset for the "far", as I modified it: Using 1 clip planes: far offset -1.5964, axis 0.032,-0.040,0.999, point 106.7,107.9,112.8)
I am trying to reproduce the view with: view matrix camera 0.051145,-0.99818,0.03201,113.43,0.99794,0.049838,-0.040387,99.325,0.038719,0.034009,0.99867,323.92 clip front 0 far -1.5964
(and varying flavors) but it doesn't recreate the same view. The clipping offset is much more drastic with my command line compared to the manual twicking of the far plane. Could you please point me in the right direction? Thank you Vincent
Le 22/08/2023 à 17:08, Elaine Meng a écrit :
Hi Vincent, You can report current clip settings in the Log with command:
clip list
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>
More to your point, however, you can save the current view (which includes the clipping plane positions) with command:
view name myviewname
....of course you can name it something else, and you can have multiple saved views with different names. Then later in the same session, either not quitting ChimeraX between, or from saving a session file after you saved the view(s) and later restoring the session from the file, you can get back to that view with command:
view myviewname
...there are various command options, like gradually moving to the view over a number of frames as is often done for recording a movie, see the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2023, at 3:34 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I opened the side view dialog window and adjusted the view planes for a nice figure. I would like to save the parameters so I can go back and modify the figure at a later stage, but the setting are not stored in the "view matrix" command. Could you tell me which command can save these settings? (I'm using chimeraX 1.5).
Thank you. Best Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/
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