Opened 3 months ago

Last modified 3 months ago

#18145 assigned defect

glTexImage3D: out of memory after ArtiaX operation

Reported by: chimerax-bug-report@… Owned by: Utz Ermel
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.5-x86_64-i386-64bit
ChimeraX Version: 1.11.dev202506260705 (2025-06-26 07:05:06 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.dev202506260705 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/clean_15.cxs format
> session

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened TS_15.rec as #1.1.1, grid size 1364,1364,400, pixel 9.12,9.12,9.12,
shown at step 1, values float32  
Log from Tue Jul 8 17:40:03 2025UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_clean2.star
> format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_clean2.star  
---  
notes | Processed as relion  
  

> artiax clip off

Opened Particle list particles_clean2.star with 5776 particles.  
Opened TS_15.rec as #1.1.1, grid size 1364,1364,400, pixel 9.12,9.12,9.12,
shown at level 0.042, step 1, values float32  

> artiax clip off

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax particles #1.2.1 originScaleFactor 3.041

> artiax view xy

> artiax particles #1.2.1 radius 22.14779412

> cd /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all

Current working directory is: /Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/clean_all.cxs

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9393,1.18e+04,2440 color #f0a3ff radius 9.12

> ui mousemode right select

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  
Drag select of 1 atoms  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_clean3.star
> partlist #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9574,1.186e+04,2440 color #f0a3ff radius 9.12

> marker #1.2.1.3 position 9224,1.182e+04,2440 color #f0a3ff radius 9.12

> marker #1.2.1.3 position 9316,1.204e+04,2440 color #f0a3ff radius 9.12

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_clean3.star
> partlist #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9266,1.167e+04,2358 color #f0a3ff radius 9.12

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9114,1.164e+04,2330 color #f0a3ff radius 9.12

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

[Repeated 1 time(s)]

> marker #1.2.1.3 position 9425,1.152e+04,2330 color #f0a3ff radius 9.12

> ui mousemode right "rotate selected particles"

> select /M:2892@M

1 atom, 1 residue, 1 model selected  

> select add /M:2893@M

2 atoms, 2 residues, 1 model selected  

> select add /M:2894@M

3 atoms, 3 residues, 1 model selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9569,1.133e+04,2221 color #f0a3ff radius 9.12

> marker #1.2.1.3 position 9489,1.127e+04,2221 color #f0a3ff radius 9.12

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  

> select /M:5784@M

1 atom, 1 residue, 1 model selected  

> select #1.2.1.2

1 model selected  

> select /M:5783@M

1 atom, 1 residue, 1 model selected  

> select /M:2899@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9007,1.131e+04,2166 color #f0a3ff radius 9.12

> marker #1.2.1.3 position 9124,1.126e+04,2166 color #f0a3ff radius 9.12

> marker #1.2.1.3 position 9406,1.124e+04,2166 color #f0a3ff radius 9.12

> marker #1.2.1.3 position 9278,1.123e+04,2166 color #f0a3ff radius 9.12

> marker #1.2.1.3 position 9411,1.125e+04,2166 color #f0a3ff radius 9.12

> select #1.1.1

3 models selected  

> ui mousemode right select

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  
Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  
Drag select of 1 atoms  

> select clear

Drag select of 1 atoms  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_clean3.star
> partlist #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9036,1.131e+04,2248 color #f0a3ff radius 9.12

> artiax particles #1.2.1 originScaleFactor 3.041

> artiax view xy

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9030,1.136e+04,2248 color #f0a3ff radius 9.12

> artiax clip off

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> partlist #1.2.1

> select clear

> select add /M:2943@M

1 atom, 1 residue, 3 models selected  

> select add /M:2928@M

2 atoms, 2 residues, 3 models selected  

> select add /M:2954@M

3 atoms, 3 residues, 3 models selected  

> select add /M:2898@M

4 atoms, 4 residues, 3 models selected  

> select add /M:2937@M

5 atoms, 5 residues, 3 models selected  

> select add /M:2936@M

6 atoms, 6 residues, 3 models selected  

> select add /M:2934@M

7 atoms, 7 residues, 3 models selected  

> select add /M:2953@M

8 atoms, 8 residues, 3 models selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9480,1.114e+04,1974 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 9340,1.109e+04,1974 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  

> select /M:3460@M

1 atom, 1 residue, 1 model selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> ui mousemode right select

> select #1.1.1

3 models selected  
Drag select of 1 atoms  

> ui mousemode right "rotate selected particles"

> select /M:3460@M

1 atom, 1 residue, 1 model selected  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> partlist #1.2.1

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/clean_15.cxs

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9522,1.175e+04,2467 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9226,1.181e+04,2440 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 9264,1.193e+04,2440 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 9441,1.183e+04,2440 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 9318,1.203e+04,2440 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

[Repeated 1 time(s)]

> select #1.2.1.2

1 model selected  

> select /M:3463@M

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9573,1.185e+04,2440 color #f0a3ff radius 12.16

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 9186,1.17e+04,2385 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.106e+04,1.116e+04,2522 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.107e+04,1.13e+04,2522 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.114e+04,1.146e+04,2522 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.104e+04,1.156e+04,2522 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.095e+04,1.146e+04,2522 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.105e+04,1.168e+04,2467 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.128e+04,1.164e+04,2467 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.121e+04,1.112e+04,2467 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.098e+04,1.159e+04,2467 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.087e+04,1.16e+04,2467 color #f0a3ff radius 12.16

> select #1.2.1.2

1 model selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> ui mousemode right select

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  
Drag select of 1 atoms  

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  

> ui mousemode right select

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  
Drag select of 1 atoms  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3473@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> select /M:3477@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.1e+04,1.171e+04,2440 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

[Repeated 1 time(s)]

> marker #1.2.1.3 position 1.128e+04,1.17e+04,2412 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.099e+04,1.067e+04,2166 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.084e+04,1.07e+04,2166 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.073e+04,1.073e+04,2166 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.063e+04,1.077e+04,2166 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3482@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3481@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3480@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.154e+04,1.116e+04,2248 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.156e+04,1.14e+04,2248 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.155e+04,1.153e+04,2248 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.147e+04,1.175e+04,2221 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.153e+04,1.151e+04,2275 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.155e+04,1.14e+04,2275 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.152e+04,1.116e+04,2275 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.139e+04,1.171e+04,2275 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #1.2.1.2

1 model selected  

> select /M:3488@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3489@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3490@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.141e+04,1.119e+04,2330 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.132e+04,1.098e+04,2330 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.135e+04,1.154e+04,2385 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.063e+04,1.126e+04,2385 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 1.047e+04,1.18e+04,2084 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.054e+04,1.187e+04,2084 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.063e+04,1.195e+04,2084 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 1.074e+04,1.203e+04,2084 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3498@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3497@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #1.2.1.2

1 model selected  

> select /M:3496@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> ui mousemode right select

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  

> select #1.1.1

3 models selected  
Drag select of axes, 1 of 714 instances, 1 atoms  

> select /M:2941@M

1 atom, 1 residue, 1 model selected  

> select /M:3007@M

1 atom, 1 residue, 1 model selected  

> select add /M:3004@M

2 atoms, 2 residues, 1 model selected  

> select add /M:2933@M

1 atom, 1 residue, 1 model selected  

> select /M:2991@M

1 atom, 1 residue, 1 model selected  

> select /M:3006@M

1 atom, 1 residue, 1 model selected  

> select /M:3003@M

1 atom, 1 residue, 1 model selected  

> select add /M:3005@M

2 atoms, 2 residues, 1 model selected  

> select add /M:3024@M

3 atoms, 3 residues, 1 model selected  

> select add /M:3023@M

1 atom, 1 residue, 1 model selected  

> select add /M:3022@M

2 atoms, 2 residues, 1 model selected  

> select add /M:3021@M

3 atoms, 3 residues, 1 model selected  

> select add /M:3025@M

4 atoms, 4 residues, 1 model selected  

> select add /M:2988@M

5 atoms, 5 residues, 1 model selected  

> select add #1.2.1.2

5 atoms, 5 residues, 2 models selected  

> select add /M:2987@M

6 atoms, 6 residues, 2 models selected  

> select add /M:2985@M

7 atoms, 7 residues, 4 models selected  

> select add /M:2986@M

8 atoms, 8 residues, 4 models selected  

> select add /M:3018@M

9 atoms, 9 residues, 4 models selected  

> select add /M:3017@M

10 atoms, 10 residues, 4 models selected  

> select add /M:3014@M

11 atoms, 11 residues, 4 models selected  

> select add /M:3015@M

12 atoms, 12 residues, 4 models selected  

> select subtract #1.2.1.2

12 atoms, 12 residues, 3 models selected  

> select add /M:3016@M

13 atoms, 13 residues, 3 models selected  

> select add #1.2.1.2

13 atoms, 13 residues, 4 models selected  

> select add /M:3027@M

14 atoms, 14 residues, 4 models selected  

> select add /M:2965@M

15 atoms, 15 residues, 4 models selected  

> select subtract #1.2.1.2

15 atoms, 15 residues, 3 models selected  

> select add /M:2972@M

16 atoms, 16 residues, 3 models selected  

> select add /M:3026@M

17 atoms, 17 residues, 3 models selected  

> select add /M:2973@M

18 atoms, 18 residues, 3 models selected  

> select add /M:2966@M

19 atoms, 19 residues, 3 models selected  

> select add /M:2967@M

20 atoms, 20 residues, 3 models selected  

> select add /M:2968@M

21 atoms, 21 residues, 3 models selected  

> select add /M:2970@M

22 atoms, 22 residues, 3 models selected  

> select add /M:2969@M

1 atom, 1 residue, 3 models selected  

> select add /M:2971@M

2 atoms, 2 residues, 3 models selected  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> ui mousemode right select

> select add /M:2949@M

1 atom, 1 residue, 3 models selected  

> select add /M:2942@M

2 atoms, 2 residues, 3 models selected  
Drag select of 1 atoms  

> select add /M:2952@M

4 atoms, 4 residues, 3 models selected  

> ui mousemode right select

Drag select of 1 atoms  
[Repeated 3 time(s)]

> select add /M:2947@M

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  
[Repeated 3 time(s)]Drag select of axes, 1 of 668 instances, 1 atoms  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> select add /M:3117@M

1 atom, 1 residue, 1 model selected  

> select add #1.2.1.2

1 atom, 1 residue, 2 models selected  

> select add /M:3041@M

2 atoms, 2 residues, 2 models selected  

> select add /M:3039@M

3 atoms, 3 residues, 2 models selected  

> select add /M:3040@M

4 atoms, 4 residues, 2 models selected  

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #1.1.1.  

> select add /M:3169@M

1 atom, 1 residue, 2 models selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8682,4155,2686 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 8644,3623,2686 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  

> select #1.2.1.2

1 model selected  
Drag select of 1 atoms  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> partlist #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8462,3387,2631 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7535,3404,2631 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 7633,3323,2631 color #f0a3ff radius 12.16

> ui mousemode right "mark plane"

> ui mousemode right "rotate selected particles"

> select /M:3503@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7433,3551,2631 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8301,4567,2494 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7422,4336,2494 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8391,3324,2385 color #f0a3ff radius 12.16

> marker #1.2.1.3 position 8265,3243,2385 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:3508@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8153,3212,2303 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> partlist #1.2.1

> select /M:3029@M

1 atom, 1 residue, 1 model selected  

> select /M:3164@M

1 atom, 1 residue, 1 model selected  

> select add /M:3029@M

2 atoms, 2 residues, 3 models selected  

> select add /M:3031@M

1 atom, 1 residue, 3 models selected  

> select add /M:3030@M

2 atoms, 2 residues, 3 models selected  

> select add #1.2.1.2

2 atoms, 2 residues, 2 models selected  

> select subtract #1.2.1.2

2 atoms, 2 residues, 1 model selected  

> select add /M:3033@M

3 atoms, 3 residues, 1 model selected  

> artiax view xy

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #1.1.1.  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> hide #!1.1.1 models

> show #!1.1.1 models

> artiax view yz

[Repeated 1 time(s)]

> artiax view xz

> artiax view xy

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 5283,5321,1728 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star  
---  
notes | Processed as relion  
  

> artiax clip off

Opened Particle list particles_TS_15.star with 672 particles.  

> artiax particles #1.2.2 originScaleFactor 3.041

> artiax view xy

> artiax particles #1.2.2 color 94,64,100,100

> ui mousemode right "mark plane"

> marker #1.2.2.3 position 5388,5762,1728 color #f0a3ff radius 12.16

> ui mousemode right "rotate selected particles"

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star  
---  
notes | Processed as relion  
  

> artiax clip off

Opened Particle list particles_TS_15.star with 672 particles.  

> artiax particles #1.2.1 originScaleFactor 3.041

> artiax view xy

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8231,4578,2686 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select #1.2.1.2

1 model selected  

> select /M:672@M

1 atom, 1 residue, 1 model selected  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> artiax hide markers

> artiax show markers

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8574,3563,2741 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select #1.2.1.2

1 model selected  
Drag select of 1 atoms  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8307,4523,2713 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select /M:674@M

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  

> select /M:674@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right rotate

> ui mousemode right select

> select /M:674@M

1 atom, 1 residue, 1 model selected  

> select /M:674@M

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  

> select clear

Drag select of axes, 1 of 675 instances, 1 atoms  

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> partlist #1.2.1

> select /M:211@M

1 atom, 1 residue, 1 model selected  

> select add /M:279@M

2 atoms, 2 residues, 1 model selected  

> select add /M:275@M

3 atoms, 3 residues, 1 model selected  

> select add /M:281@M

4 atoms, 4 residues, 1 model selected  

> select add /M:204@M

1 atom, 1 residue, 1 model selected  

> select add /M:295@M

2 atoms, 2 residues, 1 model selected  

> select add /M:296@M

3 atoms, 3 residues, 1 model selected  

> select add /M:330@M

4 atoms, 4 residues, 1 model selected  

> select add /M:329@M

5 atoms, 5 residues, 1 model selected  

> select add /M:328@M

6 atoms, 6 residues, 1 model selected  

> select add /M:194@M

7 atoms, 7 residues, 1 model selected  

> select add /M:285@M

8 atoms, 8 residues, 1 model selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8669,3719,2713 color #f0a3ff radius 36.48

> marker #1.2.1.3 position 8695,3829,2713 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select #1.2.1.2

1 model selected  

> select clear

Drag select of axes, 1 of 665 instances  
Drag select of 2 atoms  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

Drag select of 1 atoms  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8678,4115,2713 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

Drag select of axes, 2 of 666 instances, 4 atoms  
Drag select of axes, 3 of 666 instances, 4 atoms  
Drag select of axes, 1 of 666 instances, 2 atoms  

> ui mousemode right "rotate selected particles"

Drag select of axes, 1 of 666 instances, 2 atoms  
Drag select of axes, 1 of 666 instances, 1 atoms  

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> partlist #1.2.1

> select #1.1.1

3 models selected  

> select /M:252@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7729,4565,2658 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

Drag select of 2 atoms  

> select #1.2.1.2

1 model selected  

> ui mousemode right select

> select #1.2.1.2

1 model selected  

> select /M:678@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7445,4334,2549 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select /M:679@M

1 atom, 1 residue, 1 model selected  

> select /M:679@M

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 1 atoms  

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7343,3769,2549 color #f0a3ff radius 36.48

> select #1.1.1

3 models selected  

> select clear

Drag select of 1 atoms  

> ui mousemode right "rotate selected particles"

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7587,3342,2549 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  

> select /M:681@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8171,3206,2549 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

Drag select of 1 atoms  
Drag select of axes, 1 of 670 instances, 1 atoms  
[Repeated 1 time(s)]

> select clear

Drag select of 1 atoms  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/draft.em partlist
> #1.2.1

> select clear

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8724,3978,2549 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  

> select /M:683@M

1 atom, 1 residue, 1 model selected  

> select clear

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 8328,4538,2549 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select clear

Drag select of axes, 1 of 672 instances, 1 atoms  

> select clear

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7363,4231,2494 color #f0a3ff radius 36.48

> marker #1.2.1.3 position 7599,4506,2494 color #f0a3ff radius 36.48

> marker #1.2.1.3 position 7719,4571,2494 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select #1.2.1.2

1 model selected  

> select /M:687@M

1 atom, 1 residue, 1 model selected  

> select #1.1.1

3 models selected  

> select /M:686@M

1 atom, 1 residue, 1 model selected  

> select #1.1.1

3 models selected  

> select /M:685@M

1 atom, 1 residue, 1 model selected  

> select #1.1.1

3 models selected  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_TS_15.star
> partlist #1.2.1

> ui mousemode right "mark plane"

> marker #1.2.1.3 position 7691,3319,2385 color #f0a3ff radius 36.48

> marker #1.2.1.3 position 7768,3275,2385 color #f0a3ff radius 36.48

> ui mousemode right "rotate selected particles"

> select #1.1.1

3 models selected  

> select /M:689@M

1 atom, 1 residue, 1 model selected  

> select #1.1.1

3 models selected  

> select /M:688@M

1 atom, 1 residue, 1 model selected  

> select #1.1.1

3 models selected  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/clean_15.cxs

[Repeated 1 time(s)]

——— End of log from Tue Jul 8 17:40:03 2025 ———

> view name session-start

opened ChimeraX session  

> hide #!1.1.1 models

> hide #!1.2.1 models

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_clean.star
> format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL130_NEC_STA/Expand/expand_10/artiax_all/particles_clean.star  
---  
notes | Processed as relion  
  

> artiax clip off

Opened Particle list particles_clean.star with 5775 particles.  
Opened TS_17.rec as #1.1.2, grid size 1364,1364,666, pixel 9.12,9.12,9.12,
shown at level 0.0257, step 1, values float32  

> artiax clip off

> artiax tomo #1.1.2 sliceDirection 0,0,1

> artiax view xy

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage3D,  
pyArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1364,  
1364,  
666,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[ 1.48905180e-02, 9.77032445e-03, 6.30507013e-03, ...,  
-2.13987660e-03, -1.64866541e-03, 7.474934...,  
),  
cArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1364,  
1364,  
666,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[ 1.48905180e-02, 9.77032445e-03, 6.30507013e-03, ...,  
-2.13987660e-03, -1.64866541e-03, 7.474934...,  
),  
cArguments = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1364,  
1364,  
666,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[ 1.48905180e-02, 9.77032445e-03, 6.30507013e-03, ...,  
-2.13987660e-03, -1.64866541e-03, 7.474934...,  
)  
)  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 259, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1559, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1572, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 936, in draw  
drawing = self._update_view_axis(renderer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 662, in _update_view_axis  
pd = self._update_3d_texture_planes(view_dir)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 714, in _update_3d_texture_planes  
pd = self._texture_3d_planes()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 724, in _texture_3d_planes  
pd = Texture3dPlanes(self)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1551, in __init__  
self._fill_textures()  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/image3d.py", line 1668, in _fill_textures  
t.reload_texture(td, now=True)  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3210, in reload_texture  
self.fill_opengl_texture()  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3220, in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3100, in initialize_texture  
GL.glTexImage3D(gl_target, 0, iformat, size[0], size[1], size[2],  
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage3D,  
pyArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1364,  
1364,  
666,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[ 1.48905180e-02, 9.77032445e-03, 6.30507013e-03, ...,  
-2.13987660e-03, -1.64866541e-03, 7.474934...,  
),  
cArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1364,  
1364,  
666,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[ 1.48905180e-02, 9.77032445e-03, 6.30507013e-03, ...,  
-2.13987660e-03, -1.64866541e-03, 7.474934...,  
),  
cArguments = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1364,  
1364,  
666,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[ 1.48905180e-02, 9.77032445e-03, 6.30507013e-03, ...,  
-2.13987660e-03, -1.64866541e-03, 7.474934...,  
)  
)  
  
Exception ignored in: <function Drawing.__del__ at 0x1042e9440>  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1222, in __del__  
self.delete()  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1242, in delete  
raise RuntimeError("Don't have opengl context needed to delete texture from
drawing '%s' because drawing was never drawn" % self.name)  
RuntimeError: Don't have opengl context needed to delete texture from drawing
'Image3D 3d texture planes' because drawing was never drawn  
Exception ignored in: <function Texture.__del__ at 0x109fe8cc0>  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.10/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 3165, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  




OpenGL version: 4.1 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
      OS Loader Version: 583~1350

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 24 minutes, 16 seconds

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    annotated-types: 0.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.1
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.6.0
    ChimeraX-Atomic: 1.60.9
    ChimeraX-AtomicLibrary: 14.1.20
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202506260705
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.12.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.20
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.4
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.46.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 0.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    geomdl: 5.4.0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    pandas: 2.3.0
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 20.0.0
    pycollada: 0.8
    pydantic: 2.11.7
    pydantic_core: 2.33.2
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    starfile: 0.5.13
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing-inspection: 0.4.1
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by pett, 3 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → glTexImage3D: out of memory after ArtiaX operation

Conceivably should be "Third Party" instead of "Graphics"

comment:2 by Tom Goddard, 3 months ago

Component: Graphics → Third Party
Owner: changed from Tom Goddard to Utz Ermel

ArtiaX needs to limit the size of 3D volume rendering or catch the error and subsample.

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