Side View: molecule disappears on second monitor

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-13)
Description
Hi,

When the Side View window is moved to a second monitor, the molecular model disappears (the bounding box remains, and the clip planes can still be adjusted).

Cheers
Oli

Log:
> camera ortho

> cofr centerOfView

> volume voxelLimit 100000 showPlane false limitVoxelCount false
voxelLimitForOpen 10000

> alias crosshairs_on log text crosshairs_on: displays crosshairs at center of
rotation and places cofr at center of view; cofr centerofview showpivot 5,0.2

> alias crosshairs_off cofr centerofview showpivot false

> alias cootmode volume style mesh step 1 squaremesh false meshlighting true
twosidedlighting false capfaces false; surface cap false; size stickradius
0.05; ~rib; color gold target a; color byhet; lighting flat; lighting
depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set subdivision 1;
crosshairs_on; color #3333851effff target s; style stick; set bgcolor black

> alias cootmode_white volume style mesh step 1 squaremesh false meshlighting
true twosidedlighting false capfaces false; surface cap false; size
stickradius 0.05; ~rib; color orange target a; color byhet; lighting flat;
lighting depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set
subdivision 1; crosshairs_on; color #00000000cccc target s; style stick; set
bgcolor white

> alias carve surface zone #* nearatoms sel distance $1 maxcomponents 1

> alias uncarve surface unzone #*

> alias focus view cofr false

> alias saturation_down color modify $1 saturation - 10

> alias saturation_up color modify $1 saturation + 10

> alias lightness_up color modify $1 lightness + 5

> alias lightness_down color modify $1 lightness - 5

> alias hue_up color modify $1 hue + 5

> alias hue_down color modify $1 hue - 5

UCSF ChimeraX version: 0.91 (2019-06-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/oliverclarke/Dropbox/last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb

Chain information for
last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb #1  
---  
Chain | Description  
A B G I | No description available  
C D E K | No description available  
F H J O | No description available  
  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color name invisible 0,0,0,0

Color 'invisible' is 100% transparent, 0% red, 0% green, and 0% blue

  

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> help lighting

> lighting depthCueColor invisible

> select up

Nothing selected  

> color name part_invisible 0,0,0,50

Color 'part_invisible' is 50% transparent, 0% red, 0% green, and 0% blue

  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #1 part_invisible

> color "cornflower blue"

> color name part_invisible 0,0,0,90

Color 'part_invisible' is 10% transparent, 0% red, 0% green, and 0% blue

  

> color #1 part_invisible

> color name part_invisible 0,0,0,10

Color 'part_invisible' is 90% transparent, 0% red, 0% green, and 0% blue

  

> color #1 part_invisible

> color "cornflower blue"

> close all

> open /Users/oliverclarke/Dropbox/best_new_4cmc_combined_pixcorr.mrc

Opened best_new_4cmc_combined_pixcorr.mrc, grid size 512,512,512, pixel 1.06,
shown at level 0.0133, step 2, values float32  

> open
/Users/oliverclarke/Dropbox/last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb

Chain information for
last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb #2  
---  
Chain | Description  
A B G I | No description available  
C D E K | No description available  
F H J O | No description available  
  

> cootmode

Changed 151612 bond radii  
crosshairs_on: displays crosshairs at center of rotation and places cofr at
center of view  
Changed 148348 atom styles  

> toolshed show "Side View"

> help lighting

> lighting depthCueStart 0.5

> lighting depthCueEnd 0

> lighting depthCueStart 0.5

> lighting depthCueEnd 0.7

> save image /Users/oliverclarke/Dropbox/test.png width 1181 height 942
supersample 4

> save image /Users/oliverclarke/Dropbox/test.png width 1181 height 942
supersample 4

> close all

> open 1bl8

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> save image /Users/oliverclarke/Dropbox/test_1bl8.png width 1181 height 942
supersample 4

> ~ribbon

> display

> save image /Users/oliverclarke/Dropbox/test_1bl8.png width 1181 height 942
supersample 4

> close all

> open /Users/oliverclarke/Dropbox/best_new_4cmc_combined_pixcorr.mrc

Opened best_new_4cmc_combined_pixcorr.mrc, grid size 512,512,512, pixel 1.06,
shown at level 0.0133, step 2, values float32  

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> cootmode

Changed 0 bond radii  
crosshairs_on: displays crosshairs at center of rotation and places cofr at
center of view  
Changed 0 atom styles  

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> open
/Users/oliverclarke/Dropbox/last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb

Chain information for
last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb #2  
---  
Chain | Description  
A B G I | No description available  
C D E K | No description available  
F H J O | No description available  
  

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> cootmode

Changed 151612 bond radii  
crosshairs_on: displays crosshairs at center of rotation and places cofr at
center of view  
Changed 148348 atom styles  

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> hide #!1 models

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> show #!1 models

> ribbon

> ~display

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> cootmode

Changed 151612 bond radii  
crosshairs_on: displays crosshairs at center of rotation and places cofr at
center of view  
Changed 148348 atom styles  

> display

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4

> save image /Users/oliverclarke/Dropbox/test_map.png width 1181 height 942
supersample 4




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[olibclarke@…]

Clarification - referring to the molecular model in Side View disappearing, not in the main window.

Oli

[Greg Couch]

For reference, can you tell me more about how the second monitor is configured? Are both monitors plugged into the same graphics card? Or is one connected to an external GPU? And what are the models of the two monitors?

[olibclarke@…]

It is a retina iMac (27”, 2017, Radeon Pro 580 8GB GPU), with an additional HP Z27n monitor attached via a thunderbolt to HDMI connection. No external GPU.

Cheers
Oli

[Greg Couch]

I would expect that to work. If you move the ChimeraX main graphics window, so it it half on one monitor and half on the other, what do you get?

[olibclarke@…]

In that case, the side of the monitor with the largest half of the main window shows it, and the other monitor doesn’t show the smaller half at all.

Interestingly, if I move the main window to the secondary monitor and launch Side View from there, Side view looks fine on the second monitor. If I then move side view back to the primary monitor, the molecule represented in side view disappears again!

I guess maybe it is something specific to my setup?

Oli

[Greg Couch]

(FYI, no need to cc Tom and me on your replies to ChimeraX-bugs, we're both notified when information is added to the ticket.)

So yes, this bug is probably specific to your setup and the Apple graphics driver. A guess is that it might work if your external monitor supported "one billions colors" (i.e., 10-bits each for red, green, and blue), just like your retina display. Good luck!

[olibclarke@…]

Thanks - I’m actually not adding you to cc - you are already in cc when I get the email from the bug tracker, and I was just hitting reply all, but I will make sure to just reply to the ChimeraX-bugs address in future.

Cheers
Oli