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Opened 6 hours ago
Last modified 50 minutes ago
#20353 assigned defect
Torch cannot find libnvJitLink.so
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | Roden Deng Luo, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-117-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occurTraceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1459, in start_tool
return cls._get_func(api, "start_tool")(session, bi, ti)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-packages/chimerax/difffit/__init__.py", line 29, in start_tool
from . import tool
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-packages/chimerax/difffit/tool.py", line 37, in <module>
from .DiffAtomComp import diff_atom_comp, cluster_and_sort_sqd_fast, diff_fit, conv_volume, numpy2tensor, \
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-packages/chimerax/difffit/DiffAtomComp.py", line 7, in <module>
import torch
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-packages/torch/__init__.py", line 237, in <module>
from torch._C import * # noqa: F403
^^^^^^^^^^^^^^^^^^^^^^
ImportError: libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier ou dossier de ce nom
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1939, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier ou dossier de ce nom
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier ou dossier de ce nom
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /home/ferron/Documents/Projets_EM/Coronavirus/compo2/imagespourpresentation.cxs
> format session
Opened Cp2-3.08-gauche.mrc as #2, grid size 320,320,320, pixel 0.9, shown at
level 0.0349, step 2, values float32
Log from Mon May 18 22:55:53 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /home/ferron/Documents/Projets_EM/Coronavirus/nsp12RTC.cxs
Log from Thu May 14 19:01:11 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> fetch 6YYT
Unknown command: fetch 6YYT
> open 6YYT fromDatabase pdb format mmcif
Summary of feedback from opening 6YYT fetched from pdb
---
note | Fetching compressed mmCIF 6yyt from http://files.rcsb.org/download/6yyt.cif
6yyt title:
Structure of replicating SARS-CoV-2 polymerase [more info...]
Chain information for 6yyt #1
---
Chain | Description | UniProt
A | nsp12 | R1AB_SARS2 1-932
B D | nsp8 | R1AB_SARS2 1-198
C | nsp7 | R1AB_SARS2 1-83
P Q T U | RNA product |
Non-standard residues in 6yyt #1
---
ZN — zinc ion
> open 9CPO fromDatabase pdb format mmcif
Summary of feedback from opening 9CPO fetched from pdb
---
note | Fetching compressed mmCIF 9cpo from http://files.rcsb.org/download/9cpo.cif
9cpo title:
Infectious bronchitis virus core polymerase complex [more info...]
Chain information for 9cpo #2
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_IBVM 8-937
B D | Non-structural protein 8 | R1AB_IBVM 6-200
C | Non-structural protein 7 | R1AB_IBVM 2-73
P | RNA Primer |
T | RNA template |
Non-standard residues in 9cpo #2
---
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
> open 8G6R fromDatabase pdb format mmcif
Summary of feedback from opening 8G6R fetched from pdb
---
note | Fetching compressed mmCIF 8g6r from http://files.rcsb.org/download/8g6r.cif
8g6r title:
Porcine epidemic diarrhea virus core polymerase complex [more info...]
Chain information for 8g6r #3
---
Chain | Description | UniProt
A | nsp12 | A0A0U2C263_9ALPC 3-923
B | nsp8 | A0A1Z2R8Q6_9ALPC 79-192
C | nsp7 | A0A0M4AW09_9ALPC 2-63
I | RNA (5'-R(P*AP*AP*GP*AP*AP*GP*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*A)-3') |
J | RNA (5'-R(P*GP*GP*UP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*GP*CP*UP*U)-3') |
Non-standard residues in 8g6r #3
---
ZN — zinc ion
> hide #!1 models
> hide #!2 models
> open 8URB fromDatabase pdb format mmcif
Summary of feedback from opening 8URB fetched from pdb
---
note | Fetching compressed mmCIF 8urb from http://files.rcsb.org/download/8urb.cif
8urb title:
Porcine epidemic diarrhea virus complete core polymerase complex [more
info...]
Chain information for 8urb #4
---
Chain | Description | UniProt
A | nsp12 | U6BRU0_9ALPC 1-927
B D | nsp8 | U6BRU0_9ALPC 1-195
C | nsp7 | U6BRU0_9ALPC 1-83
I | RNA (33-MER) |
J | RNA (55-MER) |
Non-standard residues in 8urb #4
---
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #!2-4 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
> matchmaker #!2-4 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
> open 8URB fromDatabase pdb format mmcif
8urb title:
Porcine epidemic diarrhea virus complete core polymerase complex [more
info...]
Chain information for 8urb #5
---
Chain | Description | UniProt
A | nsp12 | U6BRU0_9ALPC 1-927
B D | nsp8 | U6BRU0_9ALPC 1-195
C | nsp7 | U6BRU0_9ALPC 1-83
I | RNA (33-MER) |
J | RNA (55-MER) |
Non-standard residues in 8urb #5
---
ZN — zinc ion
> open 9PYW fromDatabase pdb format mmcif
Summary of feedback from opening 9PYW fetched from pdb
---
notes | Fetching compressed mmCIF 9pyw from http://files.rcsb.org/download/9pyw.cif
Fetching CCD UAR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/UAR/UAR.cif
9pyw title:
SARS-CoV-2 nsp7, nsp8 and nsp12 bound to a primer-template pair with
incorporated ara-UMP [more info...]
Chain information for 9pyw #6
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
P | Primer RNA |
T | Template RNA |
Non-standard residues in 9pyw #6
---
MG — magnesium ion
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #!2-6 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
> matchmaker #!2-6 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
> matchmaker #!2-6 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
> matchmaker #!2-6 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
> open 9PZ0 fromDatabase pdb format mmcif
Summary of feedback from opening 9PZ0 fetched from pdb
---
note | Fetching compressed mmCIF 9pz0 from http://files.rcsb.org/download/9pz0.cif
9pz0 title:
SARS-CoV-2 core polymerase complex with two UTP incorporation [more info...]
Chain information for 9pz0 #7
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
P | Primer RNA |
T | Template RNA |
Non-standard residues in 9pz0 #7
---
ZN — zinc ion
> open 9PYZ fromDatabase pdb format mmcif
Summary of feedback from opening 9PYZ fetched from pdb
---
notes | Fetching compressed mmCIF 9pyz from http://files.rcsb.org/download/9pyz.cif
Fetching CCD UTP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/UTP/UTP.cif
9pyz title:
SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP [more
info...]
Chain information for 9pyz #8
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
P | Primer RNA |
T | Template RNA |
Non-standard residues in 9pyz #8
---
MG — magnesium ion
UTP — uridine 5'-triphosphate
ZN — zinc ion
> open 9CGV fromDatabase pdb format mmcif
Summary of feedback from opening 9CGV fetched from pdb
---
notes | Fetching compressed mmCIF 9cgv from http://files.rcsb.org/download/9cgv.cif
Fetching CCD A1AWQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/A1AWQ/A1AWQ.cif
9cgv title:
SARS-CoV-2 nsp12 NiRAN domain bound to a covalent inhibitor SW090466-1 [more
info...]
Chain information for 9cgv #9
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 0-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
P | RNA primer |
T | RNA template |
Non-standard residues in 9cgv #9
---
A1AWQ — methyl (8S)-7-hydroxy-5-methylpyrazolo[1,5-a]pyrimidine-3-carboxylate
MN — manganese (II) ion
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #!2-9 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
> matchmaker #!2-9 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
> open "8SQK " fromDatabase pdb format mmcif
PDB identifiers are either 4 or 8 characters long, got "8SQK "
> open 8SQK fromDatabase pdb format mmcif
Summary of feedback from opening 8SQK fetched from pdb
---
notes | Fetching compressed mmCIF 8sqk from http://files.rcsb.org/download/8sqk.cif
Fetching CCD VSN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/VSN/VSN.cif
8sqk title:
SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS,
as a pre-catalytic deRNAylation/mRNA capping intermediate [more info...]
Chain information for 8sqk #10
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 1-929
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
G | Non-structural protein 9 | R1AB_SARS2 1-113
P | Primer RNA |
T | Template RNA |
Non-standard residues in 8sqk #10
---
A — adenosine-5'-monophosphate
MG — magnesium ion
VSN — 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine
ZN — zinc ion
21 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!2-10 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
> matchmaker #!2-10 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
> hide #!3-10 atoms
> show #!3-10 cartoons
> open 7C2K fromDatabase pdb format mmcif
Summary of feedback from opening 7C2K fetched from pdb
---
notes | Fetching compressed mmCIF 7c2k from http://files.rcsb.org/download/7c2k.cif
Fetching CCD F86 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/F86/F86.cif
7c2k title:
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex [more
info...]
Chain information for 7c2k #11
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
F | RNA (29-MER) |
G | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3') |
Non-standard residues in 7c2k #11
---
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate (Remdesivir, bound form)
ZN — zinc ion
> open 7BZF fromDatabase pdb format mmcif
Summary of feedback from opening 7BZF fetched from pdb
---
note | Fetching compressed mmCIF 7bzf from http://files.rcsb.org/download/7bzf.cif
7bzf title:
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
[more info...]
Chain information for 7bzf #12
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
F | RNA (31-MER) |
G | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*A)-3') |
Non-standard residues in 7bzf #12
---
ZN — zinc ion
> open 7DTE fromDatabase pdb format mmcif
Summary of feedback from opening 7DTE fetched from pdb
---
note | Fetching compressed mmCIF 7dte from http://files.rcsb.org/download/7dte.cif
7dte title:
SARS-CoV-2 RdRP catalytic complex with T33-1 RNA [more info...]
Chain information for 7dte #13
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
F | RNA (57-MER) |
G | RNA (33-MER) |
Non-standard residues in 7dte #13
---
ZN — zinc ion
> open 9IKZ fromDatabase pdb format mmcif
Summary of feedback from opening 9IKZ fetched from pdb
---
notes | Fetching compressed mmCIF 9ikz from http://files.rcsb.org/download/9ikz.cif
Fetching CCD BEF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/BEF/BEF.cif
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif
9ikz title:
SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3- [more info...]
Chain information for 9ikz #14
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 1-931
B D | Non-structural protein 8 | R1AB_SARS2 6-192
C | Non-structural protein 7 | R1A_SARS2 1-78
E F | Helicase nsp13 | R1AB_SARS2 1-593
G | Viral protein genome-linked nsp9 | R1AB_SARS2 1-113
I | RNA (25-MER) |
J | RNA (27-MER) |
Non-standard residues in 9ikz #14
---
BEF — beryllium trifluoride ion
GDP — guanosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
32 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
> matchmaker #!2-14 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
Matchmaker 6yyt, chain A (#1) with 7c2k, chain A (#11), sequence alignment
score = 4698.1
RMSD between 840 pruned atom pairs is 0.561 angstroms; (across all 851 pairs:
0.699)
Matchmaker 6yyt, chain A (#1) with 7bzf, chain A (#12), sequence alignment
score = 4412.1
RMSD between 806 pruned atom pairs is 0.811 angstroms; (across all 838 pairs:
1.007)
Matchmaker 6yyt, chain A (#1) with 7dte, chain A (#13), sequence alignment
score = 4677.1
RMSD between 840 pruned atom pairs is 0.463 angstroms; (across all 853 pairs:
0.638)
Matchmaker 6yyt, chain A (#1) with 9ikz, chain A (#14), sequence alignment
score = 4416.4
RMSD between 830 pruned atom pairs is 0.659 angstroms; (across all 853 pairs:
0.894)
> matchmaker #!2-14 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
Matchmaker 6yyt, chain A (#1) with 7c2k, chain A (#11), sequence alignment
score = 4698.1
RMSD between 840 pruned atom pairs is 0.561 angstroms; (across all 851 pairs:
0.699)
Matchmaker 6yyt, chain A (#1) with 7bzf, chain A (#12), sequence alignment
score = 4412.1
RMSD between 806 pruned atom pairs is 0.811 angstroms; (across all 838 pairs:
1.007)
Matchmaker 6yyt, chain A (#1) with 7dte, chain A (#13), sequence alignment
score = 4677.1
RMSD between 840 pruned atom pairs is 0.463 angstroms; (across all 853 pairs:
0.638)
Matchmaker 6yyt, chain A (#1) with 9ikz, chain A (#14), sequence alignment
score = 4416.4
RMSD between 830 pruned atom pairs is 0.659 angstroms; (across all 853 pairs:
0.894)
> show #!2 models
> show #!1 models
> open 9UHT fromDatabase pdb format mmcif
Summary of feedback from opening 9UHT fetched from pdb
---
notes | Fetching compressed mmCIF 9uht from http://files.rcsb.org/download/9uht.cif
Fetching CCD GNP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif
9uht title:
SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP [more info...]
Chain information for 9uht #15
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-78
E F | Helicase nsp13 | R1AB_SARS2 1-593
G | Viral protein genome-linked nsp9 | R1AB_SARS2 1-113
H | RNA (5'-R(P*AP*UP*UP*A)-3') |
I | PRIMER |
J | TEMPLATE |
Non-standard residues in 9uht #15
---
GNP — phosphoaminophosphonic acid-guanylate ester
ZN — zinc ion
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!2-15 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
Matchmaker 6yyt, chain A (#1) with 7c2k, chain A (#11), sequence alignment
score = 4698.1
RMSD between 840 pruned atom pairs is 0.561 angstroms; (across all 851 pairs:
0.699)
Matchmaker 6yyt, chain A (#1) with 7bzf, chain A (#12), sequence alignment
score = 4412.1
RMSD between 806 pruned atom pairs is 0.811 angstroms; (across all 838 pairs:
1.007)
Matchmaker 6yyt, chain A (#1) with 7dte, chain A (#13), sequence alignment
score = 4677.1
RMSD between 840 pruned atom pairs is 0.463 angstroms; (across all 853 pairs:
0.638)
Matchmaker 6yyt, chain A (#1) with 9ikz, chain A (#14), sequence alignment
score = 4416.4
RMSD between 830 pruned atom pairs is 0.659 angstroms; (across all 853 pairs:
0.894)
Matchmaker 6yyt, chain A (#1) with 9uht, chain A (#15), sequence alignment
score = 4632.9
RMSD between 826 pruned atom pairs is 0.871 angstroms; (across all 853 pairs:
1.074)
> matchmaker #!2-15 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
Matchmaker 6yyt, chain A (#1) with 7c2k, chain A (#11), sequence alignment
score = 4698.1
RMSD between 840 pruned atom pairs is 0.561 angstroms; (across all 851 pairs:
0.699)
Matchmaker 6yyt, chain A (#1) with 7bzf, chain A (#12), sequence alignment
score = 4412.1
RMSD between 806 pruned atom pairs is 0.811 angstroms; (across all 838 pairs:
1.007)
Matchmaker 6yyt, chain A (#1) with 7dte, chain A (#13), sequence alignment
score = 4677.1
RMSD between 840 pruned atom pairs is 0.463 angstroms; (across all 853 pairs:
0.638)
Matchmaker 6yyt, chain A (#1) with 9ikz, chain A (#14), sequence alignment
score = 4416.4
RMSD between 830 pruned atom pairs is 0.659 angstroms; (across all 853 pairs:
0.894)
Matchmaker 6yyt, chain A (#1) with 9uht, chain A (#15), sequence alignment
score = 4632.9
RMSD between 826 pruned atom pairs is 0.871 angstroms; (across all 853 pairs:
1.074)
> matchmaker #!2-15 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
Matchmaker 6yyt, chain A (#1) with 7c2k, chain A (#11), sequence alignment
score = 4698.1
RMSD between 840 pruned atom pairs is 0.561 angstroms; (across all 851 pairs:
0.699)
Matchmaker 6yyt, chain A (#1) with 7bzf, chain A (#12), sequence alignment
score = 4412.1
RMSD between 806 pruned atom pairs is 0.811 angstroms; (across all 838 pairs:
1.007)
Matchmaker 6yyt, chain A (#1) with 7dte, chain A (#13), sequence alignment
score = 4677.1
RMSD between 840 pruned atom pairs is 0.463 angstroms; (across all 853 pairs:
0.638)
Matchmaker 6yyt, chain A (#1) with 9ikz, chain A (#14), sequence alignment
score = 4416.4
RMSD between 830 pruned atom pairs is 0.659 angstroms; (across all 853 pairs:
0.894)
Matchmaker 6yyt, chain A (#1) with 9uht, chain A (#15), sequence alignment
score = 4632.9
RMSD between 826 pruned atom pairs is 0.871 angstroms; (across all 853 pairs:
1.074)
> matchmaker #!2-15 to #1
Parameters
---
Chain pairing | bb
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 6yyt, chain A (#1) with 9cpo, chain A (#2), sequence alignment
score = 3006.4
RMSD between 770 pruned atom pairs is 0.871 angstroms; (across all 851 pairs:
2.046)
Matchmaker 6yyt, chain A (#1) with 8g6r, chain A (#3), sequence alignment
score = 3119.2
RMSD between 760 pruned atom pairs is 0.867 angstroms; (across all 830 pairs:
1.976)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#4), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 8urb, chain A (#5), sequence alignment
score = 3127.3
RMSD between 773 pruned atom pairs is 0.866 angstroms; (across all 852 pairs:
1.995)
Matchmaker 6yyt, chain A (#1) with 9pyw, chain A (#6), sequence alignment
score = 4659.1
RMSD between 838 pruned atom pairs is 0.690 angstroms; (across all 853 pairs:
0.837)
Matchmaker 6yyt, chain A (#1) with 9pz0, chain A (#7), sequence alignment
score = 4641.1
RMSD between 839 pruned atom pairs is 0.729 angstroms; (across all 853 pairs:
0.866)
Matchmaker 6yyt, chain A (#1) with 9pyz, chain A (#8), sequence alignment
score = 4661.5
RMSD between 838 pruned atom pairs is 0.686 angstroms; (across all 853 pairs:
0.847)
Matchmaker 6yyt, chain A (#1) with 9cgv, chain A (#9), sequence alignment
score = 4647.9
RMSD between 845 pruned atom pairs is 0.480 angstroms; (across all 853 pairs:
0.625)
Matchmaker 6yyt, chain A (#1) with 8sqk, chain A (#10), sequence alignment
score = 4539.8
RMSD between 841 pruned atom pairs is 0.681 angstroms; (across all 853 pairs:
0.830)
Matchmaker 6yyt, chain A (#1) with 7c2k, chain A (#11), sequence alignment
score = 4698.1
RMSD between 840 pruned atom pairs is 0.561 angstroms; (across all 851 pairs:
0.699)
Matchmaker 6yyt, chain A (#1) with 7bzf, chain A (#12), sequence alignment
score = 4412.1
RMSD between 806 pruned atom pairs is 0.811 angstroms; (across all 838 pairs:
1.007)
Matchmaker 6yyt, chain A (#1) with 7dte, chain A (#13), sequence alignment
score = 4677.1
RMSD between 840 pruned atom pairs is 0.463 angstroms; (across all 853 pairs:
0.638)
Matchmaker 6yyt, chain A (#1) with 9ikz, chain A (#14), sequence alignment
score = 4416.4
RMSD between 830 pruned atom pairs is 0.659 angstroms; (across all 853 pairs:
0.894)
Matchmaker 6yyt, chain A (#1) with 9uht, chain A (#15), sequence alignment
score = 4632.9
RMSD between 826 pruned atom pairs is 0.871 angstroms; (across all 853 pairs:
1.074)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 200, in run_matchmaker
ref_value = ref_widget.value
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 131, in value
return self.get_value()
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 135, in get_value
values = [self.item_map[si.text()] for si in self.selectedItems()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 135, in <listcomp>
values = [self.item_map[si.text()] for si in self.selectedItems()]
~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: '6yyt #1'
KeyError: '6yyt #1'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 135, in
values = [self.item_map[si.text()] for si in self.selectedItems()]
~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 200, in run_matchmaker
ref_value = ref_widget.value
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 131, in value
return self.get_value()
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 135, in get_value
values = [self.item_map[si.text()] for si in self.selectedItems()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 135, in <listcomp>
values = [self.item_map[si.text()] for si in self.selectedItems()]
~~~~~~~~~~~~~^^^^^^^^^^^
KeyError: '6yyt #1'
KeyError: '6yyt #1'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 135, in
values = [self.item_map[si.text()] for si in self.selectedItems()]
~~~~~~~~~~~~~^^^^^^^^^^^
See log for complete Python traceback.
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide atoms
> show cartoons
> save /home/ferron/Documents/Projets_EM/Coronavirus/nsp12RTC.cxs
——— End of log from Thu May 14 19:01:11 2026 ———
> view name session-start
opened ChimeraX session
> close session
> open /home/ferron/Documents/Projets_EM/Coronavirus/compo1droit/multichain-
> coot-3.pdb format pdb
Chain information for multichain-coot-3.pdb #1
---
Chain | Description
A | No description available
B D | No description available
C | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> open
> /home/ferron/Documents/Projets_EM/Coronavirus/compo2/Cp2-3.08-gauche.mrc
Opened Cp2-3.08-gauche.mrc as #2, grid size 320,320,320, pixel 0.9, shown at
level 0.0349, step 2, values float32
> volume #2 style mesh
> volume #2 color #1c71d8
> select add #1
23194 atoms, 23564 bonds, 1435 residues, 1 model selected
> style sel sphere
Changed 23194 atom styles
> select subtract #1
Nothing selected
> save
> /home/ferron/Documents/Projets_EM/Coronavirus/compo2/images/compo2top.png
> width 2500 height 1438 supersample 4 transparentBackground true
> save
> /home/ferron/Documents/Projets_EM/Coronavirus/compo2/images/compo2side.png
> width 2500 height 1438 supersample 4 transparentBackground true
> save
> /home/ferron/Documents/Projets_EM/Coronavirus/compo2/images/compoback.png
> width 2500 height 1438 supersample 4 transparentBackground true
> save
> /home/ferron/Documents/Projets_EM/Coronavirus/compo2/images/compo2side2.png
> width 2500 height 1438 supersample 3 transparentBackground true
> save
> /home/ferron/Documents/Projets_EM/Coronavirus/compo2/imagespourpresentation.cxs
> includeMaps true
——— End of log from Mon May 18 22:55:53 2026 ———
> view name session-start
opened ChimeraX session
> open /home/ferron/Documents/Projets_EM/Coronavirus/flip-map.mrc
Opened flip-map.mrc as #3, grid size 320,320,320, pixel 0.9, shown at level
0.111, step 2, values float32
> ui tool show EMalign
Aligning the volumes using EMalign took 22.39 seconds
Rotation:
[[0.996 -0.034 -0.083],
[-0.036 -0.999 -0.023]
[-0.083 0.025 -0.996]]
Translation:
[0.000, 0.000, -3.000]
Reflection:
0
Applying 'Fit in Map' to perform additional refinement:
Fit map flip-map.mrc in map Cp2-3.08-gauche.mrc using 40946 points
correlation = 0.9069, correlation about mean = 0.7853, overlap = 1525
steps = 128, shift = 1.42, angle = 4.82 degrees
Position of flip-map.mrc (#3) relative to Cp2-3.08-gauche.mrc (#2)
coordinates:
Matrix rotation and translation
0.99829109 0.02711647 -0.05176478 4.84603107
-0.03019190 0.99776655 -0.05958496 13.68581243
0.05003343 0.06104601 0.99688015 -15.30002533
Axis 0.71836026 -0.60621077 -0.34127267
Axis point 0.00000000 259.81219793 224.07955465
Rotation angle (degrees) 4.81637999
Shift along axis 0.40618966
\----------------------------------------------------------------------------------------
Stats before alignment:
correlation = 0.2246, correlation about mean = 0.2223, overlap = 527.694
\----------------------------------------------------------------------------------------
Stats after alignning with EMalign:
correlation = 0.5472, correlation about mean = 0.5466, overlap = 1285.713
\----------------------------------------------------------------------------------------
Stats after refining with Fit in Map:
correlation = 0.7663, correlation about mean = 0.7663, overlap = 1489.440
\----------------------------------------------------------------------------------------
> hide #!3 models
> show #!3 models
> close #2
> ui tool show DiffFit
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1459, in start_tool
return cls._get_func(api, "start_tool")(session, bi, ti)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/__init__.py", line 29, in start_tool
from . import tool
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/tool.py", line 37, in <module>
from .DiffAtomComp import diff_atom_comp, cluster_and_sort_sqd_fast, diff_fit,
conv_volume, numpy2tensor, \
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/DiffAtomComp.py", line 7, in <module>
import torch
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/torch/__init__.py", line 237, in <module>
from torch._C import * # noqa: F403
^^^^^^^^^^^^^^^^^^^^^^
ImportError: libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé:
Aucun fichier ou dossier de ce nom
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 1939, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/cmd.py",
line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in
bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier
ou dossier de ce nom
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in
bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier
ou dossier de ce nom
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show DiffFit
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1459, in start_tool
return cls._get_func(api, "start_tool")(session, bi, ti)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/__init__.py", line 29, in start_tool
from . import tool
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/tool.py", line 37, in <module>
from .DiffAtomComp import diff_atom_comp, cluster_and_sort_sqd_fast, diff_fit,
conv_volume, numpy2tensor, \
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/DiffAtomComp.py", line 7, in <module>
import torch
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/torch/__init__.py", line 237, in <module>
from torch._C import * # noqa: F403
^^^^^^^^^^^^^^^^^^^^^^
ImportError: libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé:
Aucun fichier ou dossier de ce nom
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 1939, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/cmd.py",
line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in
bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier
ou dossier de ce nom
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in
bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier
ou dossier de ce nom
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> toolshed show
Installed DiffFit (0.7.0)
> ui tool show DiffFit
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1459, in start_tool
return cls._get_func(api, "start_tool")(session, bi, ti)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/__init__.py", line 29, in start_tool
from . import tool
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/tool.py", line 37, in <module>
from .DiffAtomComp import diff_atom_comp, cluster_and_sort_sqd_fast, diff_fit,
conv_volume, numpy2tensor, \
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/difffit/DiffAtomComp.py", line 7, in <module>
import torch
File "/home/ferron/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/torch/__init__.py", line 237, in <module>
from torch._C import * # noqa: F403
^^^^^^^^^^^^^^^^^^^^^^
ImportError: libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé:
Aucun fichier ou dossier de ce nom
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 1939, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/cmd.py",
line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in
bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier
ou dossier de ce nom
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool DiffFit in
bundle DiffFit:
libnvJitLink.so.12: Ne peut ouvrir le fichier d'objet partagé: Aucun fichier
ou dossier de ce nom
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 25.2.8-0ubuntu0.24.04.1
OpenGL renderer: Mesa Intel(R) Graphics (MTL)
OpenGL vendor: Intel
Python: 3.11.13
Locale: fr_FR.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xubuntu
XDG_SESSION_DESKTOP=xubuntu
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: Dell Inc.
Model: Precision 3591
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 22 Intel(R) Core(TM) Ultra 7 155H
Cache Size: 24576 KB
Memory:
total used free shared buff/cache available
Mem: 30Gi 5.6Gi 18Gi 1.1Gi 8.0Gi 25Gi
Swap: 14Gi 0B 14Gi
Graphics:
0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Meteor Lake-P [Intel Graphics] [8086:7dd5] (rev 08)
Subsystem: Dell Meteor Lake-P [Intel Graphics] [1028:0cbb]
Kernel driver in use: i915
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2026.1.4
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.3
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.5.4
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-ProNA3D: 0.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
DiffFit: 0.7.0
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
finufft: 2.5.1
fonttools: 4.61.1
frozenlist: 1.8.0
fsspec: 2026.4.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-cublas-cu12: 12.1.3.1
nvidia-cuda-cupti-cu12: 12.1.105
nvidia-cuda-nvrtc-cu12: 12.1.105
nvidia-cuda-runtime-cu12: 12.1.105
nvidia-cudnn-cu12: 8.9.2.26
nvidia-cufft-cu12: 11.0.2.54
nvidia-curand-cu12: 10.3.2.106
nvidia-cusolver-cu12: 11.4.5.107
nvidia-cusparse-cu12: 12.1.0.106
nvidia-nccl-cu12: 2.19.3
nvidia-nvjitlink-cu12: 12.9.86
nvidia-nvtx-cu12: 12.1.105
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
torch: 2.2.1
tornado: 6.5.4
traitlets: 5.14.3
triton: 2.2.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (1)
comment:1 by , 50 minutes ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Torch cannot find libnvJitLink.so |
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