Main graphics goes gray

[alexyc991@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Whenever I move my cursor away from the structure display (left hand side), for example, to the log or the model panel on the right hand side, the display will be temporarily gone (turn gray color) until I click on it again.

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\runni\\\Desktop\\\Research\\\FYP\\\DOCKING_EM\\\STyphimuriumDNAK\\\DOCKING\\\DNAK_SCR\\\em_noPBC_clear.pdb

Summary of feedback from opening
C:\\\Users\\\runni\\\Desktop\\\Research\\\FYP\\\DOCKING_EM\\\STyphimuriumDNAK\\\DOCKING\\\DNAK_SCR\\\em_noPBC_clear.pdb  
---  
warning | Ignored bad PDB record found on line 10642  
END  
  
Chain information for em_noPBC_clear.pdb #1  
---  
Chain | Description  
| No description available  
  

> open
> C:/Users/runni/Desktop/Research/FYP/DOCKING_EM/STyphimuriumDNAK/DOCKING/DNAK_SCR/DOCKED.pdb

Summary of feedback from opening
C:/Users/runni/Desktop/Research/FYP/DOCKING_EM/STyphimuriumDNAK/DOCKING/DNAK_SCR/DOCKED.pdb  
---  
warnings | Ignored bad PDB record found on line 25  
REMARK 2 active torsions:  
  
Ignored bad PDB record found on line 26  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 27  
REMARK 1 A between atoms: C9_10 and O2_11  
  
Ignored bad PDB record found on line 28  
REMARK 2 A between atoms: C13_18 and O6_22  
  
Ignored bad PDB record found on line 31  
ROOT  
  
1195 messages similar to the above omitted  
  

> open
> C:/Users/runni/Desktop/Research/FYP/DOCKING_EM/STyphimuriumDNAK/DOCKING/DNAK_EBA/DOCKED.pdb

Summary of feedback from opening
C:/Users/runni/Desktop/Research/FYP/DOCKING_EM/STyphimuriumDNAK/DOCKING/DNAK_EBA/DOCKED.pdb  
---  
warnings | Ignored bad PDB record found on line 25  
REMARK 4 active torsions:  
  
Ignored bad PDB record found on line 26  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 27  
REMARK 1 A between atoms: C5_5 and O6_24  
  
Ignored bad PDB record found on line 28  
REMARK 2 A between atoms: C14_16 and O5_22  
  
Ignored bad PDB record found on line 29  
REMARK 3 A between atoms: C15_17 and O4_20  
  
1795 messages similar to the above omitted  
  

> open
> C:/Users/runni/Desktop/Research/FYP/DOCKING_EM/STyphimuriumDNAK/DOCKING/DNAK_XR7/DOCKED.pdb

Summary of feedback from opening
C:/Users/runni/Desktop/Research/FYP/DOCKING_EM/STyphimuriumDNAK/DOCKING/DNAK_XR7/DOCKED.pdb  
---  
warnings | Ignored bad PDB record found on line 25  
REMARK 9 active torsions:  
  
Ignored bad PDB record found on line 26  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 27  
REMARK 1 A between atoms: O1_2 and C2_3  
  
Ignored bad PDB record found on line 28  
REMARK 2 A between atoms: C3_4 and O2_5  
  
Ignored bad PDB record found on line 29  
REMARK 3 A between atoms: C7_9 and O3_10  
  
3295 messages similar to the above omitted  
  

> hide #!2 models

> show #!2 models

> hide #2

> hide #2

> hide #3

> hide #4

> select ::name="EBA"

2900 atoms, 3200 bonds, 100 models selected  

> select ::name="SCR"

2600 atoms, 2900 bonds, 100 models selected  

> open
> C:\Users\runni\Desktop\Research\FYP\DOCKING_EM\STyphimuriumDNAK\DOCKING\DNAK_SCR\em_noPBC_clear.pdb
> format pdb

Summary of feedback from opening
C:\Users\runni\Desktop\Research\FYP\DOCKING_EM\STyphimuriumDNAK\DOCKING\DNAK_SCR\em_noPBC_clear.pdb  
---  
warning | Ignored bad PDB record found on line 10642  
END  
  
Chain information for em_noPBC_clear.pdb #5  
---  
Chain | Description  
| No description available  
  

> close #5




OpenGL version: 3.3.0 NVIDIA 451.67
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Nitro AN515-43
OS: Microsoft Windows 10 Home Single Language (Build 18362)
Memory: 3,693,752,320
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 7 3750H with Radeon Vega Mobile Gfx  "
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: bug.PNG

bug.PNG​

[alexyc991@…]

Added by email2trac

[Tom Goddard]

This is very likely a problem with your graphics driver. I see you are using Nvidia 451.67 from July 9, 2020, a very recent driver. There is one newer driver Aug 17, 2020 you might try.

Are you using ChimeraX full screen? Are you using two displays? The problem is something unusual about your computer configuration.

[alexyc991@…]

Just now I've updated my Nvidia graphics driver to the latest version but
the issues still persist. I was using full screen ChimeraX not two display.

Thanks,
Alex

On Wed, Aug 26, 2020, 1:27 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

This same problem was reported 3 months ago #3239. Surprisingly that report was also with an AMD Ryzen CPU with Radeon Vega Mobile Gfx and separate Nvidia discrete graphics. ChimeraX is usng the Nvidia graphics.

Does the gray graphics happen if ChimeraX is not fullscreen?

[Tom Goddard]

I believe the reason for the gray graphics is that Windows or the ChimeraX Qt window toolkit clears the graphics to gray and then ChimeraX does not redraw the graphics. If it is cleared ChimeraX should get notified and redraw but maybe the notification is not happening or it is happening and ChimeraX somehow ignores it. I cannot reproduce this on my Windows laptop with Nvidia graphics and Intel CPU/graphics.

One test of the above theory. When the graphics becomes gray if you type a command that changes the graphics, for example, "turn" (which rotates 90 degrees), does it redraw the graphics?

[alexyc991@…]

Sorry for the late reply, I've tested using the command "turn" and it
doesn't redraw the graphics.

On Thu, 27 Aug 2020 at 01:03, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

Thanks. That is surprising that turn does not redraw the graphics because ChimeraX will always redrawing it after that command. Do you get the gray window if ChimeraX is not full screen?

[alexyc991@…]

Thanks for the update and yes, I get the gray window as well when ChimeraX
is not full screen.

On Sun, 6 Sep 2020 at 04:57, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[goddard@…]

Ok.  I'm running out of ideas how you computer does this but others don't see it.  It points to being a graphics driver issue.

Here is another thing to try.  Use the command "graphics rate on".  This will report the graphics rendering rate in the command line and will continuously redraw the graphics even when nothing has changed.

[alexyc991@…]

Yes it works, but it keeps on flashing from the graphics to gray screen.
Thanks.

[image: image.png]

On Sun, 6 Sep 2020 at 10:57, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[alexyc991@…]

Added by email2trac

[alexyc991@…]

Update: Just now I've changed the graphics settings at the NVIDIA side, of
which I've customized the preferred graphics processor specifically for
ChimeraX from "NVIDIA global setting" to "Integrated graphics".

The problem is solved now. Thanks a lot for the help.

On Sun, 6 Sep 2020 at 13:06, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

Ok. Good. But the Nvidia graphics will give better performance than the Intel integrated graphics if you are showing large structures, the will rotate and move more smoothly. But if that is not causing you trouble then the Intel graphics is fine and will not drain your laptop battery as fast. The fact that switching from nvidia to integrated graphics fixes it makes it extremely likely it is an nvidia graphics driver problem and hopefully a future nvidia driver will fix this issue.

[alexyc991@…]

Thanks a lot for the help, really appreciate that!

On Wed, 9 Sep 2020 at 06:14, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote: