[Chimera-users] Mismatch between display and saved image

[Visvaldas K.]

 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 at 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/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 at 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 at 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
>> 
>> <image_lowres.png><Screen Shot 2021-12-08 at 2.15.03 PM.png>
  
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