Hi Vis, The export code was incorrectly handling a color key that was no longer displayed. I have fixed that and the fix will be in tomorrow's build. With the fix, your session exports okay and I will send you that file separately. Some of the 2D label positions need to be tweaked (use the "Move label" right mouse mode) and the clip planes need to be adjusted to get the same kind of fading that you have in the original image, but other than that it looks mostly the same. --Eric
On Dec 9, 2021, at 12:53 AM, Visvaldas K. via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
It seems there is something hopelessly botched about the whole project. Even if delete all labels, I can't get get image right. Also, if I try to save it in Chimera (nightly build) the ChimeraX py file, it complains:
TypeError: 'NoneType' object is not iterable
File "/Applications/Chimera.app/Contents/Resources/share/chimera/chimerax.py", line 178, in write_color_key ll, ur = key.getKeyPosition()
See reply log for Python traceback.
Moreover, opening in ChimeraX-1.3 that saved py file does not open anything. When I had labels, it would just open labels without the protein. Maybe that will help to debug the problem.
Best regards,
Vis
On Wednesday, December 8, 2021, 06:17:00 PM GMT, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Vis, Maybe you didn't know that you can export a file from Chimera to open in ChimeraX, so it's not like you would need to redo everything to make a similar figure in ChimeraX.
If you get a new daily build of Chimera, the export will include the 2D labels as well as the atomic structures (atoms/ribbons). See Chimera menu: File... Export Scene, or command "export"
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>>
The export doesn't work for volume models (density maps) yet, but at least what I can see in your screenshot is atomic models, which are included.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 8, 2021, at 9:34 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Hi Vis, I haven't had this problem even using the same version of Chimera and MacOS as you, and with or without supersampling.
The image looks like the central part of the screenshot but zoomed in a lot, which is why we thought it might relate to supersampling. To help us figure it out you could use menu: Help... Report a Bug and attach your Chimera session file in which it looks like the screenshot, but image saving gives a different result. Include a brief description, including image-saving parameters you used, and your e-mail address if you want a response through the bug system.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 8, 2021, at 6:26 AM, Visvaldas K. via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Dear all,
I get a very odd mismatch between what is displayed and what is saved as a png image. I am attaching two figures, and you can probably guess what I want. Of course I will try this in ChimeraX if I am not able to fix the figure, but the image took quite some work, so I'd hate redoing it... Or I could use screenshot I guess... But certainly this is some sort of bug.
I'm using Chimera 1.15 on MacOS 12.0.1.
Thank you,
Vis
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