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#6445 closed defect (limitation)

ISOLDE/OpenMM: Error initializing context: clCreateContext

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

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.53.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open cryosparc_P9_J608_008_deepEMhancer-sharpened_tight_map_zflip.mrc

Opened cryosparc_P9_J608_008_deepEMhancer-sharpened_tight_map_zflip.mrc as #1,
grid size 450,450,450, pixel 1.35, shown at level 8.21e-05, step 2, values
float32  

> open D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb

Chain information for D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
  

> volume #1 level 0.2476

> volume #1 step 1

> clipper associate #1 toModel #2

Opened cryosparc_P9_J608_008_deepEMhancer-sharpened_tight_map_zflip.mrc as
#1.1.1.1, grid size 450,450,450, pixel 1.35, shown at level 0.271, step 1,
values float32  
Chain information for D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C 1.2/D | No description available  
  

> addh

Summary of feedback from adding hydrogens to
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb #1.2  
---  
warnings | Not adding hydrogens to /A ILE 39 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 43 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 49 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 53 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 55 CB because it is missing heavy-atom bond
partners  
140 messages similar to the above omitted  
notes | No usable SEQRES records for
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb (#1.2) chain D; guessing
termini instead  
Chain-initial residues that are actual N termini: /A PRO 36, /B SER 35, /C ILE
3, /D ILE 3  
Chain-initial residues that are not actual N termini: /A MET 425, /A LYS 471,
/A HIS 485, /B LYS 471, /B ASN 486  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 511, /A ALA 420, /A
CYS 443, /A ILE 478, /B LYS 509, /B CYS 443, /B SER 481, /C VAL 130, /D VAL
130  
679 hydrogen bonds  
Adding 'H' to /A MET 425  
Adding 'H' to /A LYS 471  
Adding 'H' to /A HIS 485  
Adding 'H' to /B LYS 471  
Adding 'H' to /B ASN 486  
/A ASN 511 is not terminus, removing H atom from 'C'  
/B LYS 509 is not terminus, removing H atom from 'C'  
/C VAL 130 is not terminus, removing H atom from 'C'  
/D VAL 130 is not terminus, removing H atom from 'C'  
8009 hydrogens added  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 48 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> set bgColor white

> volume #1.1.1.1 level 0.008465

> open
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/cryosparc_P9_J608_008_volume_map_zflipped_2.mrc

Opened cryosparc_P9_J608_008_volume_map_zflipped_2.mrc as #2, grid size
450,450,450, pixel 1.35, shown at level 0.0325, step 2, values float32  

> volume #2 step 1

> volume #2 level 1.19

> volume #2 style image

> volume #2 style surface

> volume #2 change image level -0.01477,0 level 0.03247,0.8 level 2.639,1

> transparency 0

> transparency 50

> volume #2 level 0.8538

> select clear

[Repeated 1 time(s)]

> volume #1.1.1.1 level 0.03026

Created disulphide bond between A97 and A58.  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #2 level 0.7057

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> clipper associate #2 toModel #1.2

Opened cryosparc_P9_J608_008_volume_map_zflipped_2.mrc as #1.1.1.2, grid size
450,450,450, pixel 1.35, shown at step 1, values float32  

> volume #1.1.1.2 level 0.9527

> volume #1.1.1.2 level 1.021

> isolde start

> set selectionWidth 4

Done loading forcefield  

> volume #1.1.1.2 level 0.947

> volume #1.1.1.2 level 0.4685

> volume #1.1.1.2 level 0.3945

> close #1.1.1.1

> volume #1.1.1.2 level 0.4129

> volume #1.1.1.2 level 0.5231

> volume #1.1.1.2 level 0.5537

> volume #1.1.1.2 level 0.6578

> isolde start

> set selectionWidth 4

Done loading forcefield  

> volume #1.1.1.2 level 0.6823

> volume #1.1.1.2 level 0.8721

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

> volume #1.1.1.2 level 0.8041

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/D1_A_notshapered.cxs

Taking snapshot of stepper:
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

No rotamer preview selected! Ignoring command.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  
[Repeated 1 time(s)]

> select clear

> volume #1.1.1.2 level 0.651

> select clear

[Repeated 2 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 0.9316

> volume #1.1.1.2 level 0.719

> select up

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

33 atoms, 32 bonds, 3 residues, 1 model selected  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

> select up

28 atoms, 28 bonds, 3 residues, 1 model selected  
Unable to flip peptide bond after 50 rounds. Giving up.  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up.  
[Repeated 2 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
[Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

[Repeated 1 time(s)]

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 4 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 0.6255

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 1.063

> volume #1.1.1.2 level 0.9316

> volume #1.1.1.2 level 0.8083

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/D1_A_notshapered.cxs

Taking snapshot of stepper:
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> volume #1.1.1.2 level 0.7148

> select up

46 atoms, 46 bonds, 3 residues, 1 model selected  

> select clear

[Repeated 3 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> save
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/D1-2_A_notshapered.cxs

Taking snapshot of stepper:
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  

> select clear

Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> open /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/AF-P10721-F1-model_v2.pdb

AF-P10721-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for mast/stem cell growth factor receptor
kit (P10721) [more info...]  
  
Chain information for AF-P10721-F1-model_v2.pdb #2  
---  
Chain | Description | UniProt  
A | mast/stem cell growth factor receptor kit | KIT_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #2 to #1.2/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb, chain A
(#1.2) with AF-P10721-F1-model_v2.pdb, chain A (#2), sequence alignment score
= 1955.8  
RMSD between 267 pruned atom pairs is 1.086 angstroms; (across all 439 pairs:
2.766)  
  

> select #2

4053 atoms, 4150 bonds, 513 residues, 1 model selected  

> ~select #2

Nothing selected  

> hide #2 models

> show #2 models

> hide #1.2.2 models

> show #1.2.2 models

> hide #2 models

> select clear

> show #2 models

> matchmaker #2 to #1.2/A & sel pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb, chain A
(#1.2) with AF-P10721-F1-model_v2.pdb, chain A (#2), sequence alignment score
= 465.9  
RMSD between 97 pruned atom pairs is 0.734 angstroms; (across all 103 pairs:
0.977)  
  

> select #1.2

16572 atoms, 16767 bonds, 5 pseudobonds, 1139 residues, 12 models selected  

> select #1.2

16572 atoms, 16767 bonds, 5 pseudobonds, 1139 residues, 12 models selected  

> select #1.2

16572 atoms, 16767 bonds, 5 pseudobonds, 1139 residues, 12 models selected  

> ~select #1.2.2

16572 atoms, 16767 bonds, 1139 residues, 11 models selected  

> ~select #1.2.7

16572 atoms, 16767 bonds, 1139 residues, 10 models selected  

> select #1.2.11

1 model selected  

> select clear

[Repeated 4 time(s)]

> matchmaker #2 to #1.2/A & sel pairing bs

No 'to' chains specified  

> select clear

[Repeated 4 time(s)]

> select #2

4053 atoms, 4150 bonds, 513 residues, 1 model selected  

> show sel atoms

> select clear

[Repeated 1 time(s)]

> select #2

4053 atoms, 4150 bonds, 513 residues, 1 model selected  

> hide sel cartoons

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

86 atoms, 87 bonds, 6 residues, 1 model selected  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select up

86 atoms, 85 bonds, 6 residues, 1 model selected  

> select up

156 atoms, 157 bonds, 11 residues, 1 model selected  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

82 atoms, 83 bonds, 5 residues, 1 model selected  

> select up

160 atoms, 163 bonds, 12 residues, 1 model selected  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

> select up

26 atoms, 25 bonds, 2 residues, 1 model selected  

> select up

39 atoms, 39 bonds, 2 residues, 1 model selected  

> select clear

[Repeated 4 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 1 time(s)]

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 0.6292

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/D1-2_A_notshapered.cxs

Taking snapshot of stepper:
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 5 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Created disulphide bond between A136 and A186.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
[Repeated 1 time(s)]

> volume #1.1.1.2 level 0.5977

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
[Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Created disulphide bond between A151 and A183.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 0.4

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 0.4322

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  
Must have exactly two atoms selected!  
Selected acid sidechain already has a substituent on its carboxyl group!  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/D1-3_A_notshapered.cxs

Taking snapshot of stepper:
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  

> select clear

[Repeated 4 time(s)]

> save
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/D1-3_A_notshapered.cxs

Taking snapshot of stepper:
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 0.8452

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Created disulphide bond between A233 and A290.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> hide #!1.2 models

> hide #!1.1 models

> select clear

[Repeated 3 time(s)]

> select #2

4053 atoms, 4150 bonds, 513 residues, 1 model selected  

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:201

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:201-400

1617 atoms, 1655 bonds, 200 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #2 & sel to #1.2/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
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 D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb, chain A
(#1.2) with AF-P10721-F1-model_v2.pdb, chain A (#2), sequence alignment score
= 977.3  
RMSD between 190 pruned atom pairs is 0.959 angstroms; (across all 200 pairs:
1.107)  
  

> show #!1.1 models

> show #!1.2 models

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 0.7326

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 3 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 4 time(s)]

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: paused sim  

> select clear

[Repeated 1 time(s)]ISOLDE: resumed sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

[Repeated 3 time(s)]

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]ISOLDE: Checking and correcting nomenclature for
(pseudo)symmetric side chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
Unable to flip peptide bond after 50 rounds. Giving up.  
[Repeated 1 time(s)]

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> volume #1.1.1.2 level 0.6508

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> select clear

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

ISOLDE: started sim  

> volume #1.1.1.2 level 1.016

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/app/simulation.py", line 105, in
__init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5210, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error compiling program: nvrtc: error: invalid value
for --gpu-architecture (-arch)  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2749, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2804, in
start_sim  
sm.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1611, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/app/simulation.py", line 105, in
__init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5210, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error uploading array TabulatedFunction:
clEnqueueWriteBuffer (-4)  
  
openmm.OpenMMException: Error uploading array TabulatedFunction:
clEnqueueWriteBuffer (-4)  
  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5210, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> save
> /nfs/js/krimmer/cryoEM/KIT/model_WT/P9_J608/isolde_full_model/D1-3_A_notshapered1.cxs

Taking snapshot of stepper:
D1_to_D4_SCF_fitted_into_J608_merged_D5D5-coot-17.pdb  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error compiling program: nvrtc: error: invalid value for --gpu-architecture
(-arch)  
  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/app/simulation.py", line 105, in
__init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5210, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error compiling program: nvrtc: error: invalid value
for --gpu-architecture (-arch)  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2749, in
_start_sim_or_toggle_pause  
self.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/isolde.py", line 2804, in
start_sim  
sm.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1611, in start_sim  
self._prepare_sim()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/app/simulation.py", line 105, in
__init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5210, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error initializing context: clCreateContext (-6)  
  
openmm.OpenMMException: Error initializing context: clCreateContext (-6)  
  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5210, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.94
OpenGL renderer: Quadro K4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: X9SRA/X9SRA-3
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-4820K CPU @ 3.70GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        7.7G        454M        345M        7.3G        7.1G
	Swap:          4.0G        217M        3.8G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK106GL [Quadro K4000] [10de:11fa] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:097c]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE/OpenMM: Error initializing context: clCreateContext

comment:2 by Tristan Croll, 3 years ago

Error code is CL_OUT_OF_HOST_MEMORY. I've started a discussion with the Altos software engineering team to see if they're interested in helping with more robust handling (and prevention) of CUDA/OpenCL errors like this...

comment:3 by Tristan Croll, 3 years ago

Resolution:	→ limitation
Status:	assigned → closed

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