Hi Enrico, Here are some ideas, and which may work in your case depends on the details of your system. Most are tedious. (A) if you have multiple sets of coordinates but they are all oriented the same way as each other, you could open one of those sets and experiment with "turn" over and over until you figure out the necessary commands (rotation angles and axes) to get that view starting from the initial view. E.g. keep using "view orient" to get the original view, guess some turn commands to get the view that you want, if not quite right, use "view orient" and start over. Then after you figure out the turn commands, put them in your script to use for the other sets of coordinates. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/turn.html> (B) manually (interactively) rotate one set of coordinates and save session. For each of the other sets, open that session, superimpose the new set on the one in the session using your favorite method (e.g. "matchmaker" or "align"), hide the original set. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> (C) this assembly looks like a disc shape, so perhaps it would work to define the plane of the assembly and then orient its normal along the screen Z axis (in/out). For example, with structure 1qmv open 1qmv define plane protein view orient zalign #1.1 ...where #1.1 is the model number of the plane that was created with "define plane". Still it may not align perfectly depending on the atoms used for the plane calculation. You could experiment with that, e.g. only using alpha-carbons or some other subset of the structure, for example: define plane @ca define plane :50-134 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2023, at 4:02 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I would like to perform visualisation of the pre-oriented objects from a set of PDB filles. Briefly I load 20 pbs in chimera-x and the scene what I see, is depicted on the "initial.png" image attached to the mail.
Then I need to orient it automatically in order that the scene would be perfectly parallel to the screen plane, as shown in the second enclosed image.
What options for view command could be used to orient the object in the same way ?
Many thanks in advance
Enrico <how_it_should_be.png><initial.png>