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#10182 assigned defect

ISOLDE: There is no registered Platform called "OpenCL"

Reported by:	sean.connell@…	Owned by:	Tristan Croll
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:        Linux-6.2.0-35-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /home/xhan/Downloads/ChimeraX-compare-w-8ca7-forAndreas.cxs

Opened Refinejob233-denmod_map.ccp4 as #2, grid size 114,150,120, pixel 1.05,
shown at level 1.25, step 1, values float32  
Opened emdb 16520 as #4, grid size 512,512,512, pixel 0.762, shown at level
0.025, step 1, values float32  
Opened Wilson-16520-denmod_map.ccp4 as #11, grid size 207,171,176, pixel
0.762, shown at level 1.1, step 1, values float32  
Log from Fri Nov 17 10:46:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sconnell/Desktop/ChimeraX-compare-w-8ca7-forAndreas.cxs

Opened Refinejob233-denmod_map.ccp4 as #2, grid size 114,150,120, pixel 1.05,
shown at level 1.25, step 1, values float32  
Opened emdb 16520 as #4, grid size 512,512,512, pixel 0.762, shown at level
0.025, step 1, values float32  
Opened Wilson-16520-denmod_map.ccp4 as #11, grid size 207,171,176, pixel
0.762, shown at level 1.1, step 1, values float32  
Log from Fri Nov 17 10:39:27 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open chimerax-compare-w-daniel.cxs

Opened denmod_map.ccp4 as #2, grid size 114,150,120, pixel 1.05, shown at
level 1.25, step 1, values float32  
Log from Tue Nov 14 16:14:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd /Users/sconnell/Documents/Sync-WORK/OMA

Current working directory is: /Users/sconnell/Documents/Sync-WORK/OMA  

> open phenix/RealSpaceRefine_51/ChimeraX-
> FinalMg-007-woH_real_space_refined_051.pdb

Chain information for ChimeraX-FinalMg-007-woH_real_space_refined_051.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
G | No description available  
I | No description available  
J | No description available  
M | No description available  
N | No description available  
S | No description available  
  

> open phenix-linux/ResolveCryoEM_11/denmod_map.ccp4

Opened denmod_map.ccp4 as #2, grid size 114,150,120, pixel 1.05, shown at
level 3.28, step 1, values float32  

> style stick

Changed 17271 atom styles  

> volume #2 level 1.25

> transparency #2 60

> view #1/A:U3B

> view name p1

> select zone #1/A:U3B 12 #1/A residues true

Selected 527 atoms  

> select zone #1/A:U3B 12 #1/A residues true

Selected 527 atoms  

> name frozen OMA-12-ref sel

> name list

OMA-12-ref [527 atoms, 546 bonds]  

> select clear

> save chimerax-compare-w-daniel.cxs includeMaps true compress gzip

——— End of log from Tue Nov 14 16:14:16 2023 ———

opened ChimeraX session  

> lighting simple

> open 8ca7 fromDatabase pdb

8ca7 title:  
Omadacycline and spectinomycin bound to the 30S ribosomal subunit head [more
info...]  
  
Chain information for 8ca7 #3  
---  
Chain | Description | UniProt  
A | 16S rRNA |  
C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233  
E | Small ribosomal subunit protein uS5 | RS5_ECOLI 1-167  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130  
J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103  
M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118  
N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101  
S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92  
  
Non-standard residues in 8ca7 #3  
---  
2MG — 2N-methylguanosine-5'-monophosphate  
4OC — 4N,O2'-methylcytidine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
K — potassium ion  
MG — magnesium ion  
SCM — spectinomycin (actinospectacin; espectinomicina; CHX-3101)  
U3B — Omadacycline (Omadacycline;
(4S,4aS,5aR,12aR)-4,7-bis(dimethylamino)-9-[(2,2-dimethylpropylamino)methyl]-1,10,11,12a-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide)  
  

> open 16520 fromDatabase emdb

Opened emdb 16520 as #4, grid size 512,512,512, pixel 0.762, shown at level
1.41e-05, step 2, values float32  

> open 8cf1 fromDatabase pdb

8cf1 title:  
Tetracycline bound to the 30S head [more info...]  
  
Chain information for 8cf1 #5  
---  
Chain | Description | UniProt  
A | 16S rRNA |  
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241  
C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233  
E | Small ribosomal subunit protein uS5 | RS5_ECOLI 1-167  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130  
J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103  
M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118  
N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101  
S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92  
  
Non-standard residues in 8cf1 #5  
---  
2MG — 2N-methylguanosine-5'-monophosphate  
4OC — 4N,O2'-methylcytidine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
K — potassium ion  
MG — magnesium ion  
TAC — tetracycline  
  

> open 16615 fromDatabase emdb

Summary of feedback from opening 16615 fetched from emdb  
---  
note | Fetching compressed map 16615 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16615/map/emd_16615.map.gz  
  
Opened emdb 16615 as #6, grid size 800,800,800, pixel 0.681, shown at step 1,
values float32  

> open 8cf8 fromDatabase pdb

8cf8 title:  
Eravacycline bound to the 30S head [more info...]  
  
Chain information for 8cf8 #7  
---  
Chain | Description | UniProt  
A | 16S rRNA |  
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241  
C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130  
J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103  
M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118  
N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101  
S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92  
  
Non-standard residues in 8cf8 #7  
---  
2MG — 2N-methylguanosine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
K — potassium ion  
MG — magnesium ion  
YQM — Eravacycline  
  

> open 16620 fromDatabase emdb

Summary of feedback from opening 16620 fetched from emdb  
---  
note | Fetching compressed map 16620 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16620/map/emd_16620.map.gz  
  
Opened emdb 16620 as #8, grid size 600,600,600, pixel 0.768, shown at level
8.59e-06, step 4, values float32  

> open 8cgi fromDatabase pdb

8cgi title:  
Pentacycline TP038 bound to the 30S head [more info...]  
  
Chain information for 8cgi #9  
---  
Chain | Description | UniProt  
4 | Large ribosomal subunit protein bL31A | RL31_ECOLI 1-70  
A | 16S rRNA |  
C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130  
J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103  
M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118  
N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101  
S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92  
  
Non-standard residues in 8cgi #9  
---  
2MG — 2N-methylguanosine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
K — potassium ion  
MG — magnesium ion  
P8F — Pentacycline
((4S,4aS,5aR,14aS)-4-(dimethylamino)-10-[(3-fluoranylazetidin-1-yl)methyl]-3,12,14,14a-tetrakis(oxidanyl)-1,13-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-pentacene-2-carboxamide;
Pentacycline TP-038)  
  

> open 16644 fromDatabase emdb

Summary of feedback from opening 16644 fetched from emdb  
---  
note | Fetching compressed map 16644 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16644/map/emd_16644.map.gz  
  
Opened emdb 16644 as #10, grid size 480,480,480, pixel 0.757, shown at level
2.02e-05, step 2, values float32  

> style #1,3,5,7,9 stick

Changed 91198 atom styles  

> volume #4 level 0.025 step 1 transparency 0.6 style surface

> volume #6 region 0,0,0,799,799,799 step 1 level 0.025 transparency 0.6 style
> surface

> volume #8 level 0.012 step 1 transparency 0.6 style surface

> volume #10 level 0.015 step 1 transparency 0.6 style surface

> mmaker #3/A to OMA-12-ref matrix Nucleic bring #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChimeraX-FinalMg-007-woH_real_space_refined_051.pdb, chain A (#1)
with 8ca7, chain A (#3), sequence alignment score = 87.8  
RMSD between 23 pruned atom pairs is 0.229 angstroms; (across all 23 pairs:
0.229)  
  

> mmaker #5/A to OMA-12-ref matrix Nucleic bring #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChimeraX-FinalMg-007-woH_real_space_refined_051.pdb, chain A (#1)
with 8cf1, chain A (#5), sequence alignment score = 87.8  
RMSD between 23 pruned atom pairs is 0.216 angstroms; (across all 23 pairs:
0.216)  
  

> mmaker #7/A to OMA-12-ref matrix Nucleic bring #8

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChimeraX-FinalMg-007-woH_real_space_refined_051.pdb, chain A (#1)
with 8cf8, chain A (#7), sequence alignment score = 87.8  
RMSD between 23 pruned atom pairs is 0.229 angstroms; (across all 23 pairs:
0.229)  
  

> mmaker #9/A to OMA-12-ref matrix Nucleic bring #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChimeraX-FinalMg-007-woH_real_space_refined_051.pdb, chain A (#1)
with 8cgi, chain A (#9), sequence alignment score = 87.8  
RMSD between 23 pruned atom pairs is 0.217 angstroms; (across all 23 pairs:
0.217)  
  

> view p1

executed chimerax-compare-w-daniel-script.cxc  

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> open /Users/sconnell/Documents/Sync-WORK/OMA/phenix-
> linux/ResolveCryoEM_40/denmod_map.ccp4

Opened denmod_map.ccp4 as #11, grid size 207,171,176, pixel 0.762, shown at
level 1.92, step 1, values float32  

> open 8ca7 fromDatabase pdb

8ca7 title:  
Omadacycline and spectinomycin bound to the 30S ribosomal subunit head [more
info...]  
  
Chain information for 8ca7 #12  
---  
Chain | Description | UniProt  
A | 16S rRNA |  
C | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233  
E | Small ribosomal subunit protein uS5 | RS5_ECOLI 1-167  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
I | Small ribosomal subunit protein uS9 | RS9_ECOLI 1-130  
J | Small ribosomal subunit protein uS10 | RS10_ECOLI 1-103  
M | Small ribosomal subunit protein uS13 | RS13_ECOLI 1-118  
N | Small ribosomal subunit protein uS14 | RS14_ECOLI 1-101  
S | Small ribosomal subunit protein uS19 | RS19_ECOLI 1-92  
  
Non-standard residues in 8ca7 #12  
---  
2MG — 2N-methylguanosine-5'-monophosphate  
4OC — 4N,O2'-methylcytidine-5'-monophosphate  
5MC — 5-methylcytidine-5'-monophosphate  
K — potassium ion  
MG — magnesium ion  
SCM — spectinomycin (actinospectacin; espectinomicina; CHX-3101)  
U3B — Omadacycline (Omadacycline;
(4S,4aS,5aR,12aR)-4,7-bis(dimethylamino)-9-[(2,2-dimethylpropylamino)methyl]-1,10,11,12a-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide)  
  

> hide #!11 models

> select add #12

18093 atoms, 18881 bonds, 700 pseudobonds, 1935 residues, 4 models selected  

> style sel stick

Changed 18093 atom styles  

> select subtract #12

Nothing selected  

> mmaker #12/A to OMA-12-ref matrix Nucleic bring #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ChimeraX-FinalMg-007-woH_real_space_refined_051.pdb, chain A (#1)
with 8ca7, chain A (#12), sequence alignment score = 87.8  
RMSD between 23 pruned atom pairs is 0.229 angstroms; (across all 23 pairs:
0.229)  
  

> show #!11 models

> hide #!12 models

> volume #11 level 1.2

> volume #11 level 1.1

> transparency #11 60

> hide #!2 models

> hide #!1 models

> show #!12 models

> volume resample #11 onGrid #2

Opened denmod_map.ccp4 resampled as #13, grid size 114,150,120, pixel 1.05,
shown at step 1, values float32  

> close #13

> close #5-10

> show #!11 models

> show #!1 models

> hide #!1 models

> rename #2 Refinedenmod_map.ccp4

> show #!3 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> hide #!3 models

> show #!3 models

> rename #2 Refinejob233-denmod_map.ccp4

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!3 models

> rename #11 Wilson-16520-denmod_map.ccp4

> show #!12 models

> hide #!12 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> save ChimeraX-compare-w-8ca7-forAndreas.cxs includeMaps true compress gzip

——— End of log from Fri Nov 17 10:39:27 2023 ———

opened ChimeraX session  

> show #!2 models

> hide #!11 models

> show #!11 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> show #!1 models

> hide #!3 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!11 models

> show #!3 models

> close #12

> save ChimeraX-compare-w-8ca7-forAndreas.cxs includeMaps true compress gzip

——— End of log from Fri Nov 17 10:46:16 2023 ———

opened ChimeraX session  

> select zone #1/A:U3B 4 #1 residues true

Selected 201 atoms  

> color sel lime

> lighting simple

> hide #!3 models

> lighting simple

[Repeated 2 time(s)]

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> lighting simple

[Repeated 6 time(s)]

> isolde start

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 101 residues in model #1 to IUPAC-IUB
standards.  

> clipper associate #11 toModel #1

Opened Wilson-16520-denmod_map.ccp4 as #1.1.1.1, grid size 207,171,176, pixel
0.762, shown at step 1, values float32  

> lighting simple

[Repeated 1 time(s)]

> select zone #1/A:U3B 4 #1 residues true

Selected 201 atoms, 1 surfaces  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2  
---  
warning | Not adding hydrogens to ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/A G 927 P because it is
missing heavy-atom bond partners  
notes | No usable SEQRES records for ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb (#1.2) chain C; guessing termini
instead  
No usable SEQRES records for ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb (#1.2) chain G; guessing termini
instead  
No usable SEQRES records for ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb (#1.2) chain I; guessing termini
instead  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/B LEU 97, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/C GLY 2, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/G PRO 2, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/I ASN 4, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/J ARG 5, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/M ALA 2, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/N ALA 2, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/S PRO 2  
Chain-initial residues that are not actual N termini: ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/G VAL 94  
Chain-final residues that are actual C termini: ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/B ASP 153, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/C ILE 207, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/G GLU 129, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/I SER 128, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/J LEU 102, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/M ILE 116, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/N TRP 101, ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/S ALA 85  
Chain-final residues that are not actual C termini: ChimeraX-
FinalMg-007-woH_real_space_refined_051.pdb #1.2/G VAL 69  
2692 hydrogen bonds  
Adding 'H' to ChimeraX-FinalMg-007-woH_real_space_refined_051.pdb #1.2/G VAL
94  
12841 hydrogens added  
  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  

> select zone #1/A:U3B 4 #1 residues true

Selected 313 atoms, 1 surfaces  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde ignore #1/A:1600

ISOLDE: currently ignoring 1 residues in model 1.2  

> isolde ignore #1/C:1347

> select zone #1/A:U3B 4 #1 residues true

Selected 313 atoms, 1 surfaces  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde ignore #1/C:347

ISOLDE: currently ignoring 2 residues in model 1.2  

> select zone #1/A:U3B 4 #1 residues true

Selected 313 atoms  

> isolde sim start sel

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error initializing CUDA: CUDA_ERROR_COMPAT_NOT_SUPPORTED_ON_DEVICE (804) at
/home/tcroll/openmm_build_env/openmm/platforms/cuda/src/CudaContext.cpp:140  

Traceback (most recent call last):  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1409, in start_sim  
self._prepare_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1367, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error initializing CUDA:
CUDA_ERROR_COMPAT_NOT_SUPPORTED_ON_DEVICE (804) at
/home/tcroll/openmm_build_env/openmm/platforms/cuda/src/CudaContext.cpp:140  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 894, in start_sim  
sm.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 398, in start_sim  
sh.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1414, in start_sim  
self._prepare_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1354, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 894, in start_sim  
sm.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 398, in start_sim  
sh.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1409, in start_sim  
self._prepare_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1354, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 906, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1793, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  

> select zone #1/A:U3B

Missing or invalid "range" argument: Expected a number  

> select #1/A:U3B

82 atoms, 85 bonds, 1 residue, 1 model selected  

> isolde sim start sel

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 894, in start_sim  
sm.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 398, in start_sim  
sh.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1409, in start_sim  
self._prepare_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1354, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
  
See log for complete Python traceback.  
  

> lighting simple

[Repeated 2 time(s)]

> isolde sim start sel

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 894, in start_sim  
sm.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 398, in start_sim  
sh.start_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1409, in start_sim  
self._prepare_sim()  
File "/home/xhan/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1354, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 23.0.4-0ubuntu1~22.04.1
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:2
Manufacturer: Hewlett-Packard
Model: HP Z440 Workstation
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz
Cache Size: 10240 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       5.8Gi        44Gi       107Mi        12Gi        56Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GP104 [GeForce GTX 1070] [1043:8596]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.20.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.dev1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.1.7
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (1)

comment:1 by Eric Pettersen, 2 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE: There is no registered Platform called "OpenCL"

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