ChimeraX bug report submission

[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,

A couple of minor UI glitches with the Settings panel:

* The Settings panel behaves as a dockable tool - I don't think it should be, at least not by default, and unlike the other tools there doesn't seem to be a way to disable this behavior (no context menu appears when one right clicks the docked panel).

* In the Startup tab, the text entry box is really narrow, and does not resize when the window is resized. Also, the scroll bar is very glitchy on Mac - when I attempt to scroll using the trackpad, the scroll bar in the text entry box jumps to the left and covers half the text.

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.