Opened 18 months ago

Closed 12 months ago

#15103 closed defect (can't reproduce)

map.volume._update_drawings: KeyError

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-89-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/6s59/segger_mod_segs/10099_6s59_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/6s59/segger_mod_segs/10099_6s59_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/6s59/segger_mod_segs/10099_6s59_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/6s59/segger_mod_segs/10099_6s59_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/6s59/segger_mod_segs/10099_6s59_1.mrc

Opened 10099_6s59_5.mrc as #1.1, grid size 26,24,22, pixel 1, shown at level
1, step 1, values float32  
Opened 10099_6s59_4.mrc as #1.2, grid size 28,20,30, pixel 1, shown at level
1, step 1, values float32  
Opened 10099_6s59_3.mrc as #1.3, grid size 12,12,12, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 10099_6s59_2.mrc as #1.4, grid size 12,16,16, pixel 1, shown at level
1, step 1, values float32  
Opened 10099_6s59_1.mrc as #1.5, grid size 14,12,12, pixel 1, shown at level
1, step 1, values float32  

> open 6s59

Summary of feedback from opening 6s59 fetched from pdb  
---  
warning | Atom SG has no neighbors to form bonds with according to residue
template for CYS /B:804  
  
6s59 title:  
Structure of ovine transhydrogenase in the apo state [more info...]  
  
Chain information for 6s59 #2  
---  
Chain | Description | UniProt  
A B | Nicotinamide nucleotide transhydrogenase | W5PFI3_SHEEP -42-1043  
  
Non-standard residues in 6s59 #2  
---  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
  

> volume #1.1 level 0.001892

> volume #1.2 level 0.03499

> volume #1.4 level 0.01294

> volume #1.5 level 0.009208

> hide atoms

> hide cartoons

> select ::name="PC1"

309 atoms, 301 bonds, 8 residues, 1 model selected  

> show sel atoms

> transparency 50

> volume #1.4 level 0

> close #1

> close #2

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_1.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_6.ccp4
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_6.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_7.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_8.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_9.mrc

Opened 26956_8crr_1.mrc as #1, grid size 16,24,18, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_2.mrc as #2, grid size 18,16,22, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_3.mrc as #3, grid size 18,24,20, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_4.mrc as #4, grid size 18,20,32, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_5.mrc as #5, grid size 30,36,36, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_6.ccp4 as #6, grid size 40,42,40, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_6.mrc as #7, grid size 40,42,40, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_7.mrc as #8, grid size 22,22,30, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_8.mrc as #9, grid size 30,30,48, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_9.mrc as #10, grid size 14,16,16, pixel 1, shown at level 1,
step 1, values float32  

> volume #1 level 0.02394

> volume #2 level 0.0111

> volume #3 level 0.01842

> volume #4 level 0.01478

> volume #5 level 0.02578

> volume #6 level 0.04236

> volume #7 level 0.9982

> volume #7 level 0.05525

> volume #8 level 0.0332

> volume #9 level 0.03315

> volume #10 level 0.02767

> open 8crr

8crr title:  
Local refinement of Band 3-III transmembrane domains, class 1 of erythrocyte
ankyrin-1 complex [more info...]  
  
Chain information for 8crr #11  
---  
Chain | Description | UniProt  
B D | Glycophorin-A | GLPA_HUMAN 1-150  
C E | Band 3 anion transport protein | B3AT_HUMAN 1-911  
  
Non-standard residues in 8crr #11  
---  
CLR — cholesterol  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)  
  

> hide atoms

> hide cartoons

> select ::name="CLR"::name="NAG"::name="PIO"

206 atoms, 214 bonds, 8 residues, 1 model selected  

> show sel atoms

> transparency 50

> volume #2 level 1

> close #1-11

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_1.ccp4
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_1.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_6.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_7.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_8.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_9.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_10.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_11.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_12.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_13.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_14.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_15.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_16.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_17.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_18.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_19.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_20.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_21.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_22.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_23.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_24.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_25.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_26.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_27.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_28.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cte/segger_mod_segs/26988_8cte_29.mrc

Opened 26988_8cte_1.ccp4 as #1, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26988_8cte_1.mrc as #2, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26988_8cte_2.mrc as #3, grid size 20,16,14, pixel 1, shown at level 1,
step 1, values float32  
Opened 26988_8cte_3.mrc as #4, grid size 18,16,16, pixel 1, shown at level 1,
step 1, values float32  
Opened 26988_8cte_4.mrc as #5, grid size 16,20,16, pixel 1, shown at level 1,
step 1, values float32  
Opened 26988_8cte_5.mrc as #6, grid size 12,10,12, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26988_8cte_6.mrc as #7, grid size 28,26,22, pixel 1, shown at level 1,
step 1, values float32  
Opened 26988_8cte_7.mrc as #8, grid size 16,16,20, pixel 1, shown at level 1,
step 1, values float32  
Opened 26988_8cte_8.mrc as #9, grid size 14,22,22, pixel 1, shown at level 1,
step 1, values float32  
Opened 26988_8cte_9.mrc as #10, grid size 20,20,16, pixel 1, shown at level 1,
step 1, values float32  
Opened 26988_8cte_10.mrc as #11, grid size 30,28,26, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_11.mrc as #12, grid size 26,20,16, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_12.mrc as #13, grid size 16,18,14, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26988_8cte_13.mrc as #14, grid size 22,22,16, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_14.mrc as #15, grid size 14,20,28, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_15.mrc as #16, grid size 22,28,24, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_16.mrc as #17, grid size 22,34,20, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_17.mrc as #18, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26988_8cte_18.mrc as #19, grid size 20,18,28, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26988_8cte_19.mrc as #20, grid size 34,36,32, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_20.mrc as #21, grid size 36,40,34, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_21.mrc as #22, grid size 24,26,38, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_22.mrc as #23, grid size 40,32,18, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_23.mrc as #24, grid size 36,24,40, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_24.mrc as #25, grid size 18,18,28, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_25.mrc as #26, grid size 38,44,30, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_26.mrc as #27, grid size 54,46,44, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_27.mrc as #28, grid size 14,14,14, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_28.mrc as #29, grid size 22,12,16, pixel 1, shown at level
1, step 1, values float32  
Opened 26988_8cte_29.mrc as #30, grid size 20,18,22, pixel 1, shown at level
1, step 1, values float32  

> open 8cte

8cte title:  
Class 2 of erythrocyte ankyrin-1 complex (Composite map) [more info...]  
  
Chain information for 8cte #31  
---  
Chain | Description | UniProt  
A | Ankyrin-1 | ANK1_HUMAN 1-1881  
D N | Glycophorin-A | GLPA_HUMAN 1-150  
K | Blood group Rh(CE) polypeptide | RHCE_HUMAN 1-417  
L Q | Ammonium transporter Rh type A | RHAG_HUMAN 1-409  
M O R S | Aquaporin-1 | AQP1_HUMAN 1-269  
P T W | Band 3 anion transport protein | B3AT_HUMAN 1-911  
X | Protein 4.2 | EPB42_HUMAN 1-691  
  
Non-standard residues in 8cte #31  
---  
AJP — Digitonin  
CLR — cholesterol  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)  
  

> hide atoms

> hide cartoons

> select ::name="AJP"::name="CLR"::name="NAG"::name="PIO"

477 atoms, 518 bonds, 16 residues, 1 model selected  

> show sel atoms

> volume style surface

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume #7 level 0,0 level 0.1,0.8 level 1,1

> volume #22 level 0,0 level 0.1,0.8 level 1,1

> volume #23 level 0,0 level 0.1,0.8 level 1,1

> volume #23 style surface

> volume #23 level 1

> volume #29 style surface

> volume #29 change image level 0,0 level 0.1,0.8 level 1,1

> volume #29 level 0.8619

> close #1-31

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_1.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_6.ccp4
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_6.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_7.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_8.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8crr/segger_mod_segs/26956_8crr_9.mrc

Opened 26956_8crr_1.mrc as #1, grid size 16,24,18, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_2.mrc as #2, grid size 18,16,22, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_3.mrc as #3, grid size 18,24,20, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_4.mrc as #4, grid size 18,20,32, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_5.mrc as #5, grid size 30,36,36, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_6.ccp4 as #6, grid size 40,42,40, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_6.mrc as #7, grid size 40,42,40, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_7.mrc as #8, grid size 22,22,30, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_8.mrc as #9, grid size 30,30,48, pixel 1, shown at level 1,
step 1, values float32  
Opened 26956_8crr_9.mrc as #10, grid size 14,16,16, pixel 1, shown at level 1,
step 1, values float32  

> open 8crr

8crr title:  
Local refinement of Band 3-III transmembrane domains, class 1 of erythrocyte
ankyrin-1 complex [more info...]  
  
Chain information for 8crr #11  
---  
Chain | Description | UniProt  
B D | Glycophorin-A | GLPA_HUMAN 1-150  
C E | Band 3 anion transport protein | B3AT_HUMAN 1-911  
  
Non-standard residues in 8crr #11  
---  
CLR — cholesterol  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)  
  

> hide atoms

> hide cartoons

> select ::name="CLR"::name="NAG"::name="PIO"

206 atoms, 214 bonds, 8 residues, 1 model selected  

> show sel atoms

> volume style surface

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume style surface

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume #2 level 0,0 level 0.1,0.8 level 1,1

> volume #6 level 0,0 level 0.1,0.8 level 1,1

> volume #8 level 0,0 level 0.1,0.8 level 1,1

> volume #7 style surface

> volume #7 change image level 0,0 level 0.1,0.8 level 1,1

> volume #7 level 0.06082

> transparency 50

> close #1-11

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/5wc0/segger_mod_segs/8794_5wc0_1.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/5wc0/segger_mod_segs/8794_5wc0_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/5wc0/segger_mod_segs/8794_5wc0_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/5wc0/segger_mod_segs/8794_5wc0_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/5wc0/segger_mod_segs/8794_5wc0_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/5wc0/segger_mod_segs/8794_5wc0_6.mrc

Opened 8794_5wc0_1.mrc as #1.1, grid size 30,34,20, pixel 1, shown at level 1,
step 1, values float32  
Opened 8794_5wc0_2.mrc as #1.2, grid size 20,26,32, pixel 1, shown at level 1,
step 1, values float32  
Opened 8794_5wc0_3.mrc as #1.3, grid size 26,18,18, pixel 1, shown at level 1,
step 1, values float32  
Opened 8794_5wc0_4.mrc as #1.4, grid size 34,26,28, pixel 1, shown at level 1,
step 1, values float32  
Opened 8794_5wc0_5.mrc as #1.5, grid size 22,20,22, pixel 1, shown at level 1,
step 1, values float32  
Opened 8794_5wc0_6.mrc as #1.6, grid size 20,24,20, pixel 1, shown at level 1,
step 1, values float32  

> open 5wc0

5wc0 title:  
katanin hexamer in spiral conformation [more info...]  
  
Chain information for 5wc0 #2  
---  
Chain | Description | UniProt  
A B C D E F | Meiotic spindle formation protein mei-1 | KTNA1_CAEEL 1-472  
  
Non-standard residues in 5wc0 #2  
---  
ATP — adenosine-5'-triphosphate  
  

> hide atoms

> hide cartoons

> select ::name="ATP"

186 atoms, 198 bonds, 6 residues, 1 model selected  

> show sel atoms

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume #1.3 level 0,0 level 0.1,0.8 level 1,1

> close #1-2#1.1-6

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_1.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_6.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_7.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_8.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_9.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_10.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_11.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_12.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8bxf/segger_mod_segs/16317_8bxf_13.mrc

Opened 16317_8bxf_1.mrc as #1.1, grid size 16,16,16, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_2.mrc as #1.2, grid size 28,24,22, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_3.mrc as #1.3, grid size 38,34,22, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_4.mrc as #1.4, grid size 28,34,22, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_5.mrc as #1.5, grid size 34,16,20, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_6.mrc as #1.6, grid size 12,14,16, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_7.mrc as #1.7, grid size 18,16,16, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_8.mrc as #1.8, grid size 14,14,14, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_9.mrc as #1.9, grid size 14,18,14, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_10.mrc as #1.10, grid size 30,28,22, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 16317_8bxf_11.mrc as #1.11, grid size 20,20,16, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_12.mrc as #1.12, grid size 28,34,22, pixel 1, shown at level
1, step 1, values float32  
Opened 16317_8bxf_13.mrc as #1.13, grid size 24,26,22, pixel 1, shown at level
1, step 1, values float32  

> open 8bxf

Summary of feedback from opening 8bxf fetched from pdb  
---  
note | Fetching compressed mmCIF 8bxf from
http://files.rcsb.org/download/8bxf.cif  
  
8bxf title:  
Alvinella pompejana nicotinic acetylcholine receptor Alpo4 in apo state
(Alpo4_apo, dataset 1) [more info...]  
  
Chain information for 8bxf #2  
---  
Chain | Description  
A B C D E | Acetylcholine receptor  
  
Non-standard residues in 8bxf #2  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> hide atoms

> hide cartoons

> select ::name="NAG"

70 atoms, 70 bonds, 5 residues, 1 model selected  

> show sel atoms

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

> volume #1.10 level 0,0 level 0.1,0.8 level 1,1

> volume #1.3 level 0,0 level 0.1,0.8 level 1,1

> volume #1.3 style surface

> volume #1.3 level 1

[Repeated 1 time(s)]

> transparency 50

> close #1-2

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_1.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_6.ccp4
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_6.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_7.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_8.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_9.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_10.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_11.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_12.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_13.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_14.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_15.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_16.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_17.ccp4
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_17.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_18.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_19.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_20.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_21.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_22.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_23.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_24.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_25.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_26.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_27.ccp4
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_27.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_28.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_29.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_30.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_31.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_32.ccp4
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_32.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_33.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_34.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_35.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_36.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_37.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/8cs9/segger_mod_segs/26960_8cs9_38.mrc

Opened 26960_8cs9_1.mrc as #1, grid size 12,14,12, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_2.mrc as #2, grid size 16,22,14, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_3.mrc as #3, grid size 20,18,16, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_4.mrc as #4, grid size 20,16,22, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_5.mrc as #5, grid size 24,20,18, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_6.ccp4 as #6, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26960_8cs9_6.mrc as #7, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26960_8cs9_7.mrc as #8, grid size 18,20,16, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_8.mrc as #9, grid size 22,20,16, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_9.mrc as #10, grid size 18,22,24, pixel 1, shown at level 1,
step 1, values float32  
Opened 26960_8cs9_10.mrc as #11, grid size 22,22,18, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_11.mrc as #12, grid size 18,14,16, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_12.mrc as #13, grid size 18,26,18, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_13.mrc as #14, grid size 22,18,18, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_14.mrc as #15, grid size 26,18,18, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_15.mrc as #16, grid size 12,12,14, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_16.mrc as #17, grid size 34,26,18, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_17.ccp4 as #18, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26960_8cs9_17.mrc as #19, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26960_8cs9_18.mrc as #20, grid size 34,22,24, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_19.mrc as #21, grid size 30,22,16, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_20.mrc as #22, grid size 14,22,12, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_21.mrc as #23, grid size 32,26,40, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_22.mrc as #24, grid size 24,36,36, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_23.mrc as #25, grid size 46,40,38, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_24.mrc as #26, grid size 34,44,20, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_25.mrc as #27, grid size 12,12,14, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26960_8cs9_26.mrc as #28, grid size 42,50,28, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_27.ccp4 as #29, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26960_8cs9_27.mrc as #30, grid size 10,10,10, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 26960_8cs9_28.mrc as #31, grid size 22,36,24, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_29.mrc as #32, grid size 38,34,24, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_30.mrc as #33, grid size 22,26,24, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_31.mrc as #34, grid size 44,48,42, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_32.ccp4 as #35, grid size 40,54,42, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_32.mrc as #36, grid size 40,54,42, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_33.mrc as #37, grid size 20,24,14, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_34.mrc as #38, grid size 36,34,28, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_35.mrc as #39, grid size 18,20,24, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_36.mrc as #40, grid size 14,16,14, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_37.mrc as #41, grid size 14,12,12, pixel 1, shown at level
1, step 1, values float32  
Opened 26960_8cs9_38.mrc as #42, grid size 16,16,16, pixel 1, shown at level
1, step 1, values float32  

> hide #!23 models

> show #!23 models

> volume #23 level 0.3591

> open 8cs9

8cs9 title:  
Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex [more
info...]  
  
Chain information for 8cs9 #43  
---  
Chain | Description | UniProt  
A | Ankyrin-1 | ANK1_HUMAN 1-1881  
K | Blood group Rh(CE) polypeptide | RHCE_HUMAN 1-417  
L Q | Ammonium transporter Rh type A | RHAG_HUMAN 1-409  
P | Glycophorin-B | GLPB_HUMAN 1-91  
R S T a b c | Glycophorin-A | GLPA_HUMAN 1-150  
V Y Z e f g | Band 3 anion transport protein | B3AT_HUMAN 1-911  
X | Protein 4.2 | EPB42_HUMAN 1-691  
  
Non-standard residues in 8cs9 #43  
---  
AJP — Digitonin  
CLR — cholesterol  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)  
  

> hide atoms

> hide cartoons

> select ::name="AJP"::name="CLR"::name="HOH"::name="NAG"::name="PIO"

974 atoms, 741 bonds, 295 residues, 1 model selected  

> show sel atoms

> transparency 50

> volume #37 level 0

[Repeated 1 time(s)]

> volume #37 level 0.0442

> volume #23 level 0

> volume #8 region 0,0,0,17,19,15

> volume #23 level 0.005525

> volume #23 level 0

> volume #23 level 0.0001

> volume #23 level 1e-15

> volume #23 level 0

> volume #23 level 0.003683

> close #1-43

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/old_results/7xzh_suffix/segmented/33527_7xzh_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/old_results/7xzh_suffix/segmented/33527_7xzh_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/old_results/7xzh_suffix/segmented/33527_7xzh_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/old_results/7xzh_suffix/segmented/33527_7xzh_1.mrc

Opened 33527_7xzh_4.mrc as #1.1, grid size 50,58,132, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 33527_7xzh_3.mrc as #1.2, grid size 58,58,124, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_2.mrc as #1.3, grid size 54,60,130, pixel 1, shown at level
5e-05, step 1, values float32  
Opened 33527_7xzh_1.mrc as #1.4, grid size 40,46,76, pixel 1, shown at level
1, step 1, values float32  

> close #1#1.1-4

> open
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_23.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_22.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_21.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_20.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_19.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_18.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_17.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_16.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_15.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_14.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_13.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_12.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_11.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_10.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_9.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_8.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_7.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_6.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_5.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_4.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_3.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_2.mrc
> /net/kihara/scratch/jain488/CryoLig_c/CryoEM_Lig/Dataset/Dataset_codes/test_lig_fit/Genkis_method/full_pipeline/code_final/bell/segger_mod_all/7xzh/segger_mod_segs/33527_7xzh_1.mrc

Opened 33527_7xzh_23.mrc as #1.1, grid size 20,26,26, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_22.mrc as #1.2, grid size 30,40,30, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_21.mrc as #1.3, grid size 28,26,26, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_20.mrc as #1.4, grid size 18,24,28, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_19.mrc as #1.5, grid size 22,24,24, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_18.mrc as #1.6, grid size 26,30,32, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_17.mrc as #1.7, grid size 26,24,30, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_16.mrc as #1.8, grid size 22,22,26, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_15.mrc as #1.9, grid size 36,34,32, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_14.mrc as #1.10, grid size 28,30,30, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_13.mrc as #1.11, grid size 28,42,26, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_12.mrc as #1.12, grid size 16,18,16, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_11.mrc as #1.13, grid size 28,34,30, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_10.mrc as #1.14, grid size 26,26,30, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_9.mrc as #1.15, grid size 28,24,30, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_8.mrc as #1.16, grid size 16,16,16, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_7.mrc as #1.17, grid size 12,12,16, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_6.mrc as #1.18, grid size 16,14,16, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_5.mrc as #1.19, grid size 16,16,16, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_4.mrc as #1.20, grid size 14,14,16, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_3.mrc as #1.21, grid size 14,14,16, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_2.mrc as #1.22, grid size 14,18,14, pixel 1, shown at level
1, step 1, values float32  
Opened 33527_7xzh_1.mrc as #1.23, grid size 16,16,16, pixel 1, shown at level
1, step 1, values float32  

> volume region all imageMode "full region"

> volume unzone

> mousemode rightMode "crop volume"

Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e58796ed0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79d83690>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e9e35ce50>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79d80dd0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e9e35fcd0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e9e258cd0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79d81cd0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79defcd0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e9e35dc90>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e9e35dc10>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e58795410>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79dec3d0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79deda90>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79def210>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e58794fd0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e9e259990>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79ded990>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e58794150>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e58794110>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e79d80110>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e9e2598d0>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
KeyError: <chimerax.map.volume.Volume object at 0x7f1e58797850>  
  
Error processing trigger "graphics update":  
KeyError:  
  
File "/apps/chimerax/1.7.1-jammy/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 4059, in _update_drawings  
vset.remove(v)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.223.02
OpenGL renderer: NVIDIA GeForce GT 710/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: Super Server
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            94Gi        20Gi       2.6Gi       162Mi        70Gi        71Gi
	Swap:             0B          0B          0B

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK208B [GeForce GT 710] [10de:128b] (rev a1)	
	Subsystem: PNY GK208B [GeForce GT 710] [196e:118b]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-OpenCommands: 1.1.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (3)

comment:1 by Eric Pettersen, 18 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → map.volume._update_drawings: KeyError

comment:2 by Tom Goddard, 18 months ago

It appears the VolumeUpdateManager._update_drawings method had volumes unexpectedly removed from the set that needs updating. The only place the get removed from the set is in this same _update_drawings method, so apparently it was called recursively. That happens during the "graphics update" trigger. That trigger happens off a timer that should only be called when Qt enters the event loop. Actually an UpdateLoop.update_graphics_now() call will also do it. That must be what happened.

I can make the _update_drawings() call ignore recursive calls. But I should think about whether "graphics update" and "new frame" calls outside the the Qt timer callback could cause other havoc.

comment:3 by Tom Goddard, 12 months ago

Resolution: → can't reproduce
Status: assigned → closed

This is the only report of this error in many years using update_graphics_now(). Will consider fixes if it is ever reported again.

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