Something wrong with clipping for large models

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-16)
Description
Clipping seems to work as expected for small structures, but goes rather pear-shaped for large structures (see screen recording).

For large structures or EM maps (e.g. 5TAQ, EMD-8382), instead of showing a flat surface at the clip plane, ChimeraX shows an ambiently-lit "ghost" of the map or molecule. Very strange. I don't think it used to do this in earlier versions.

Cheers
Oli

Log:
UCSF ChimeraX version: 0.8 (2018-11-16)  
How to cite UCSF ChimeraX  

> open
/Users/oliverclarke/Dropbox/Documents/Work/Projects/RyR/ryr_paper_3/structures_and_maps/cam_maps_and_models/tet_moved.pdb

Chain information for tet_moved.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  
  

> clip

> camera ortho

> 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)  
  
  

> clip

> clip off

> surface #1

> clip

> close all

> open 5taq

5taq title:  
Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 3&4) [more info...]  
  
Chain information for 5taq #1  
---  
Chain | Description  
A F H J | Peptidyl-prolyl cis-trans isomerase FKBP1B  
B E G I | Ryanodine receptor 1  
  
  

> clip

> clip off

> ribbon

> ~display

> clip

> 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)  
  
  

Expected a keyword  

> clip

> clip off

> surface #1

> clip

> close

> open 5taq

5taq title:  
Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 3&4) [more info...]  
  
Chain information for 5taq #1  
---  
Chain | Description  
A F H J | Peptidyl-prolyl cis-trans isomerase FKBP1B  
B E G I | Ryanodine receptor 1  
  
  

> clip

> clip off

> surface

> clip

> close

> open 8382 fromDatabase emdb

Opened emd_8382.map, grid size 400,400,400, pixel 1.25, shown at level 0.0174,
step 2, values float32  

> clip




OpenGL version: 4.1 ATI-2.2.8
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: chimerax_clipping_bug.mov

chimerax_clipping_bug.mov​

[olibclarke@…]

Added by email2trac

[Tom Goddard]

Fixed.

Clipping was broken depending on the display style and lighting mode, not the size of the model.

Clipping was broken since a graphics change Sept 18, almost 2 months ago. I guess no one is using clipping.