Opened 2 years ago

Closed 2 years ago

#9477 closed defect (wontfix)

Networks: libbz2.so.1.0: cannot open shared object file: No such file or directory

Reported by: pradip.singh@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard, Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.92.1.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.  

> open /nfs/home/pksingh/DATA/BfpE_1/BfpDEC_01.cxs

Log from Wed Jul 26 16:10:23 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/RealSpaceRefine_21/J184-218_PilB-
> pkAF_modeld.cxs

Opened J184_218_PilBpk_fit.mrc as #2, grid size 226,226,226, pixel 1.08, shown
at level 0.15, step 1, values float32  
Log from Wed Jul 26 14:27:13 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockPredictedModel_17/J184_218_PilBpk_fit_docked.pdb

Chain information for J184_218_PilBpk_fit_docked.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/J184_218_PilBpk_fit.mrc

Opened J184_218_PilBpk_fit.mrc as #2, grid size 226,226,226, pixel 1.08, shown
at level 0.15, step 1, values float32  

> volume #2 style mesh

> color #1 #fce94f transparency 0

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockPredictedModel_19/J184_218_PilBpk_fit_docked.pdb

Chain information for J184_218_PilBpk_fit_docked.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #!2 models

> show #!2 models

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockPredictedModel_20/J184_218_PilBpk_fit_docked.pdb

Chain information for J184_218_PilBpk_fit_docked.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #!2 models

> hide #3 models

> show #3 models

> show #1 models

> show #!2 models

> hide #!2 models

> open
> /nfs/home/pksingh/DATA/PilB_Pak_analysis_clean_files/PilB_pak_ApplyNCS_hexamer_ref1-coot-0.pdb

Chain information for PilB_pak_ApplyNCS_hexamer_ref1-coot-0.pdb #5  
---  
Chain | Description  
A B C D E F | No description available  
  

> hide atoms

> show cartoons

> color #5 #d3d7cf transparency 0

> color #5 #8ae234 transparency 0

> color #5 #3465a4 transparency 0

> close #5

> close #4

> show #!2 models

> save
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/RealSpaceRefine_21/TwoChain_comb_PilBpk.pdb
> relModel #2

> save
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/RealSpaceRefine_21/J184-218_PilBpkfit.mrc
> models #2

> save
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/RealSpaceRefine_21/J184-218_PilB-
> pkAF_modeld.cxs

> save
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/RealSpaceRefine_21/J184-218_PilB-
> pkAF_modeld.cxs includeMaps true

——— End of log from Wed Jul 26 14:27:13 2023 ———

opened ChimeraX session  

> transparency #2 50

> close

> open /nfs/home/pksingh/DATA/AlphaFold_BfpD-E-C/prediction_6/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /A

2000 atoms, 2041 bonds, 251 residues, 1 model selected  

> color sel red

> select /B

1280 atoms, 1307 bonds, 164 residues, 1 model selected  

> color sel forest green

> select /C

4248 atoms, 4318 bonds, 535 residues, 1 model selected  

> color sel light sea green

> hide #1 models

> show #1 models

> select #1

7528 atoms, 7666 bonds, 950 residues, 1 model selected  

> ~select #1

Nothing selected  

> ui tool show "Build Structure"

> toolshed show

> color bypolymer

[Repeated 1 time(s)]

> color bychain

> ~hbonds

> open /nfs/home/pksingh/DATA/BfpE_1/best_model_MTRIX_expanded.pdb

Chain information for best_model_MTRIX_expanded.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #2 models

> hide #1 models

> show #2 models

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_full_docked.pdb

Summary of feedback from opening
/nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_full_docked.pdb  
---  
warning | Ignored bad PDB record found on line 1033  
  
Chain information for composite_map_full_docked.pdb #3  
---  
Chain | Description  
A1 | No description available  
  

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_hs.pdb

Summary of feedback from opening
/nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_hs.pdb  
---  
warning | Ignored bad PDB record found on line 2973  
  
Chain information for composite_map_hs.pdb #4  
---  
Chain | Description  
U | No description available  
  

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_docked.pdb

Summary of feedback from opening
/nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_docked.pdb  
---  
warning | Ignored bad PDB record found on line 1033  
  
Chain information for composite_map_docked.pdb #5  
---  
Chain | Description  
A1 | No description available  
  

> open
> /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_processed.pdb

Summary of feedback from opening
/nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/Phenix_184/DockAndRebuild_29/composite_map_processed.pdb  
---  
warning | Ignored bad PDB record found on line 1033  
  
Chain information for composite_map_processed.pdb #6  
---  
Chain | Description  
A1 | No description available  
  

> close #6

> close #5

> close #4

> close #3

> view orient

> open /nfs/home/pksingh/DATA/Other_PilB_Str/BfpD_map_pdb/8dzg.pdb

8dzg.pdb title:  
Cryo-em structure of bundle-forming pilus extension atpase from E.coli In the
presence of adp [more info...]  
  
Chain information for 8dzg.pdb #3  
---  
Chain | Description | UniProt  
A B C D E F | BFPD | Q47070_ECOLX  
  
Non-standard residues in 8dzg.pdb #3  
---  
ADP — adenosine-5'-diphosphate  
MG — magnesium ion  
ZN — zinc ion  
  

> close #2

> show #1 models

> ui tool show Matchmaker

> matchmaker #!3 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 best_model.pdb, chain C (#1) with 8dzg.pdb, chain A (#3), sequence
alignment score = 2046.7  
RMSD between 269 pruned atom pairs is 0.781 angstroms; (across all 420 pairs:
5.873)  
  

> matchmaker #!3 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 best_model.pdb, chain C (#1) with 8dzg.pdb, chain A (#3), sequence
alignment score = 2046.7  
RMSD between 269 pruned atom pairs is 0.781 angstroms; (across all 420 pairs:
5.873)  
  

> hide atoms

> show cartoons

> color #3 #c4a000 transparency 0

> color #3 #5c3566 transparency 0

> color #3 #babdb6 transparency 0

> color #3 #8f5902 transparency 0

> color #3 salmon transparency 0

> color #3 #b2b2ff transparency 0

> color #3 #204a87 transparency 0

> save /nfs/home/pksingh/DATA/BfpE_1/BfpDEC_01.cxs

——— End of log from Wed Jul 26 16:10:23 2023 ———

opened ChimeraX session  

> show target m

> log metadata #1,3

No models had metadata

> log chains #1,3

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Chain information for 8dzg.pdb #3  
---  
Chain | Description | UniProt  
A B C D E F | BFPD | Q47070_ECOLX  
  

> hide #!3 models

> ui mousemode right select

Drag select of 46 residues  

> select #1/C:162

5 atoms, 4 bonds, 1 residue, 1 model selected  
Drag select of 20 residues  
Drag select of 14 residues  
Drag select of 24 residues  
Drag select of 1 residues  

> ui mousemode right distance

> style sel stick

Changed 227 atom styles  

> show sel atoms

> hbonds sel reveal true

45 hydrogen bonds found  

> ui mousemode right select

[Repeated 1 time(s)]

> select clear

> interfaces #1 & ~solvent

2 buried areas: C B 1049, C A 862  
Traceback (most recent call last):  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/toolbar/tool.py",
line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run  
f(s)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/cmd.py", line 49, in interfaces  
tool.ContactPlot(session, sg, ba, interface_residue_area_cutoff)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 25, in __init__  
Graph.__init__(self, session, groups, contacts,  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/graph.py", line 139, in __init__  
self.graph = self._make_graph()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/graph.py", line 160, in _make_graph  
import networkx as nx  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/networkx/__init__.py",
line 57, in <module>  
from networkx import utils  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/networkx/utils/__init__.py", line 2, in <module>  
from networkx.utils.decorators import *  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/networkx/utils/decorators.py", line 12, in <module>  
import re, gzip, bz2  
File "/opt/chimerax-1.3/lib/python3.9/bz2.py", line 18, in <module>  
from _bz2 import BZ2Compressor, BZ2Decompressor  
ImportError: libbz2.so.1.0: cannot open shared object file: No such file or
directory  
  
ImportError: libbz2.so.1.0: cannot open shared object file: No such file or
directory  
  
File "/opt/chimerax-1.3/lib/python3.9/bz2.py", line 18, in  
from _bz2 import BZ2Compressor, BZ2Decompressor  
  
See log for complete Python traceback.  
  

> ui mousemode right select

Drag select of 266 residues  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select clear

Drag select of 28 residues  

> show sel atoms

> hbonds sel reveal true

38 hydrogen bonds found  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for best_model.pdb_B SES surface #1.1: minimum, -12.00, mean
-0.47, maximum 16.00  
Coulombic values for best_model.pdb_C SES surface #1.2: minimum, -20.61, mean
-1.28, maximum 16.53  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> hide #!1 surfaces

> ui mousemode right select

Drag select of 74 atoms, 25 residues, 64 bonds, 14 pseudobonds  

> select clear

Drag select of 22 atoms, 11 residues, 17 bonds, 7 pseudobonds  
Drag select of 2 atoms, 3 residues, 4 bonds, 1 pseudobonds  
Drag select of 21 atoms, 3 residues, 20 bonds, 1 pseudobonds  
Drag select of 12 atoms, 2 residues, 10 bonds  
Drag select of 1 residues, 1 pseudobonds  

> color bfactor sel

71 atoms, 14 residues, 2 surfaces, atom bfactor range 75.1 to 91.7  

> style sel ball

Changed 71 atom styles  

> ui mousemode right select

Drag select of 28 atoms, 20 residues, 23 bonds, 12 pseudobonds  

> hbonds sel reveal true

22 hydrogen bonds found  

> ~hbonds

> ui mousemode right select

> select #1/B:22@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:22@CD1

1 atom, 1 residue, 1 model selected  
Drag select of 12 atoms, 1 residues, 13 bonds  

> hide sel atoms

> show sel cartoons

[Repeated 1 time(s)]

> show sel atoms

> ui mousemode right select

Drag select of 102 atoms, 45 residues, 91 bonds  

> hide sel atoms

> select clear

> ui mousemode right select

Drag select of 31 residues  

> color bfactor sel

257 atoms, 31 residues, 2 surfaces, atom bfactor range 53.5 to 92.2  

> color bfactor sel

257 atoms, 31 residues, 2 surfaces, atom bfactor range 53.5 to 92.2  

> color bfactor sel

257 atoms, 31 residues, 2 surfaces, atom bfactor range 53.5 to 92.2  

> color sel bychain

Drag select of 12 residues  

> color sel bychain

> select clear

Drag select of 9 residues  

> show sel atoms

Drag select of 4 residues  

> show sel atoms

> select clear

Drag select of 3 residues  
Drag select of 1 residues  
Drag select of 1 atoms, 4 residues, 1 bonds  

> select add #1/B:23

33 atoms, 4 bonds, 5 residues, 3 models selected  

> show sel atoms

> select #1/B:22

14 atoms, 15 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add #1/B:110

22 atoms, 22 bonds, 2 residues, 2 models selected  

> hide sel atoms

> select clear

> select add #1/C:67@CD

1 atom, 1 residue, 1 model selected  

> select clear

> select add #1/C:67

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

> select add #1/C:60

19 atoms, 18 bonds, 2 residues, 2 models selected  

> select add #1/C:71

30 atoms, 28 bonds, 3 residues, 2 models selected  

> select add #1/C:68

38 atoms, 35 bonds, 4 residues, 2 models selected  

> select add #1/C:63

47 atoms, 43 bonds, 5 residues, 2 models selected  

> select add #1/B:109

58 atoms, 54 bonds, 6 residues, 2 models selected  

> select add #1/B:21

66 atoms, 61 bonds, 7 residues, 3 models selected  

> select add #1/B:107

73 atoms, 67 bonds, 8 residues, 3 models selected  

> select add #1/B:108@CA

74 atoms, 67 bonds, 9 residues, 3 models selected  

> select subtract #1/B:108

73 atoms, 67 bonds, 8 residues, 3 models selected  

> select add #1/B:108

83 atoms, 77 bonds, 9 residues, 3 models selected  

> select add #1/C:64

91 atoms, 84 bonds, 10 residues, 3 models selected  

> select add #1/C:61

99 atoms, 91 bonds, 11 residues, 3 models selected  

> select add #1/B:23

103 atoms, 94 bonds, 12 residues, 3 models selected  

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> show sel atoms

> select #1/B:22

14 atoms, 15 bonds, 1 residue, 1 model selected  

> undo

> select add #1/B:22

117 atoms, 109 bonds, 13 residues, 3 models selected  

> show sel atoms

> hbonds sel reveal true

20 hydrogen bonds found  

> select subtract #1/B:22

103 atoms, 94 bonds, 12 residues, 3 models selected  

> select clear

> select #1/B:22

14 atoms, 15 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/C:68

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

> select clear

> select #1/C:64

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

> select #1/C:67

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

> select #1/C:65

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

> show sel atoms

> hide sel atoms

> select clear

> undo

[Repeated 9 time(s)]

> select add #1/C:71

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #1/C:68

19 atoms, 17 bonds, 2 residues, 2 models selected  

> select add #1/C:64

27 atoms, 24 bonds, 3 residues, 2 models selected  

> select add #1/C:67

36 atoms, 32 bonds, 4 residues, 2 models selected  

> select add #1/B:19

44 atoms, 39 bonds, 5 residues, 2 models selected  

> select add #1/C:60

54 atoms, 49 bonds, 6 residues, 3 models selected  

> select #1/A

2000 atoms, 2041 bonds, 251 residues, 1 model selected  

> hide sel cartoons

> select add #1/C:60

2010 atoms, 2051 bonds, 252 residues, 1 model selected  

> select add #1/B:57@CA

2011 atoms, 2051 bonds, 253 residues, 2 models selected  

> select add #1/B:56

2020 atoms, 2059 bonds, 254 residues, 2 models selected  

> select add #1/B:24

2026 atoms, 2064 bonds, 255 residues, 3 models selected  

> select subtract #1/B:57

2025 atoms, 2064 bonds, 254 residues, 3 models selected  

> select add #1/B:57

2034 atoms, 2072 bonds, 255 residues, 3 models selected  

> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select add #1/B:19

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

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select add #1/C:71@NE

9 atoms, 10 bonds, 2 residues, 2 models selected  

> select add #1/C:71@CG

10 atoms, 12 bonds, 2 residues, 3 models selected  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #1/b

1280 atoms, 1307 bonds, 11 pseudobonds, 164 residues, 2 models selected  

> select #1/b:24

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ~label (#!1 & sel) residues

> select #1/c:60

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> ui mousemode right clip

> select #1/b

1280 atoms, 1307 bonds, 11 pseudobonds, 164 residues, 2 models selected  

> color (#!1 & sel) magenta

> select #1/a

2000 atoms, 2041 bonds, 251 residues, 1 model selected  

> select #1/c

4248 atoms, 4318 bonds, 7 pseudobonds, 535 residues, 2 models selected  

> color (#!1 & sel) forest green

> ~select #1.2

4318 bonds, 7 pseudobonds, 3 models selected  

> set bgColor white

> ui mousemode right select

Drag select of 7 residues  
Drag select of 11 residues  

> show sel atoms

> hbonds sel reveal true

20 hydrogen bonds found  

> undo

[Repeated 2 time(s)]Undo failed, probably because structures have been
modified.  
Drag select of 8 atoms, 2 residues, 9 bonds  

> select clear

Drag select of 6 atoms, 6 bonds  

> hbonds sel reveal true

1 hydrogen bonds found  
Drag select of 1 atoms, 3 residues  

> hbonds sel reveal true

8 hydrogen bonds found  
Drag select of 1 atoms, 2 residues  

> hbonds sel reveal true

5 hydrogen bonds found  
Drag select of 1 atoms, 4 residues  
Drag select of 1 residues, 1 bonds  

> hbonds sel reveal true

10 hydrogen bonds found  

> select #1/b/56

1280 atoms, 1307 bonds, 164 residues, 1 model selected  

> ~label (#!1 & sel) residues

Drag select of 1 atoms  
Drag select of 1 residues, 1 bonds  
Drag select of 2 atoms, 1 residues, 1 bonds  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

Drag select of 2 atoms, 2 residues, 2 bonds  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select clear

Drag select of 1 residues, 1 bonds  

> select #1/b/57

1280 atoms, 1307 bonds, 164 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #1/b/57

1280 atoms, 1307 bonds, 164 residues, 1 model selected  

> ~label (#!1 & sel) residues

> undo

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

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

Drag select of 2 atoms, 1 residues, 1 bonds  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #1/c

4248 atoms, 4318 bonds, 8 pseudobonds, 535 residues, 2 models selected  

> select #1/a

2000 atoms, 2041 bonds, 251 residues, 1 model selected  

> show sel cartoons

> ~label sel residues

> select clear

[Repeated 1 time(s)]

> ui mousemode right clip

> select #1/b

1280 atoms, 1307 bonds, 164 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> ui mousemode right select

Drag select of 100 atoms, 106 residues, 86 bonds, 8 pseudobonds  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> ui mousemode right rotate

> ui mousemode right select

Drag select of 99 atoms, 40 residues, 81 bonds  

> hbonds sel reveal true

52 hydrogen bonds found  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ~label (#!1 & sel) residues

> select clear

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select add #1/C:176

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

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select add #1/C:174

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select add #1/A:228

24 atoms, 21 bonds, 3 residues, 2 models selected  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ui mousemode right clip

[Repeated 1 time(s)]

> ui mousemode right "clip rotate"

> ui mousemode right clip

> ui mousemode right select

> select add #1/C:166

32 atoms, 28 bonds, 4 residues, 2 models selected  

> select add #1/A:191

40 atoms, 35 bonds, 5 residues, 2 models selected  

> select add #1/A:192

48 atoms, 42 bonds, 6 residues, 2 models selected  

> select subtract #1/A:191

40 atoms, 35 bonds, 5 residues, 2 models selected  

> ui mousemode right clip

[Repeated 1 time(s)]

> ui mousemode right zone

[Repeated 1 time(s)]

> view

> view sel

> ui tool show "Side View"

> ui mousemode right zone

> select #1

7528 atoms, 7666 bonds, 50 pseudobonds, 950 residues, 3 models selected  

> ~select #1

2 models selected  

> ui mousemode right zone

[Repeated 1 time(s)]

> ui mousemode right clip

> ui mousemode right select

> select clear

[Repeated 5 time(s)]

> ui mousemode right zone

> hide #1.3 models

> hide #1.2 models

> hide #1.1 models

> hide #!1 models

> hide #2 models

> show #!1 models

> show #1.1 models

> show #1.2 models

> show #1.3 models

> show #2 models

> show #!3 models

> ui mousemode right "clip rotate"

> show cartoons

> show atoms

> close #1.2

> close

> open /nfs/home/pksingh/DATA/BfpE_1/BfpDEC_01.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 691, in restore  
self.reset()  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 535, in reset  
sm.reset_state(container, self)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/tools.py",
line 292, in reset_state  
tool_inst.delete()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
Traceback (most recent call last):  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 691, in restore  
self.reset()  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 535, in reset  
sm.reset_state(container, self)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/tools.py",
line 292, in reset_state  
tool_inst.delete()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 433, in collated_open  
return remember_data_format()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 995, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 733, in restore  
self.reset()  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 535, in reset  
sm.reset_state(container, self)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/tools.py",
line 292, in reset_state  
tool_inst.delete()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
  
See log for complete Python traceback.  
  

> open /nfs/home/pksingh/DATA/BfpE_1/BfpDEC_01.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 691, in restore  
self.reset()  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 535, in reset  
sm.reset_state(container, self)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/tools.py",
line 292, in reset_state  
tool_inst.delete()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
Traceback (most recent call last):  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 691, in restore  
self.reset()  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 535, in reset  
sm.reset_state(container, self)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/tools.py",
line 292, in reset_state  
tool_inst.delete()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 433, in collated_open  
return remember_data_format()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 995, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 733, in restore  
self.reset()  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/session.py",
line 535, in reset  
sm.reset_state(container, self)  
File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/core/tools.py",
line 292, in reset_state  
tool_inst.delete()  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
AttributeError: 'ContactPlot' object has no attribute '_handler'  
  
File "/opt/chimerax-1.3/lib/python3.9/site-
packages/chimerax/interfaces/tool.py", line 47, in delete  
atomic.get_triggers(self._session()).remove_handler(self._handler)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.56
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: X10SRA
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
Cache Size: 15360 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        9.7G        3.6G        126M        2.0G        5.2G
	Swap:          7.5G         79M        7.4G

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P5000] [10de:1bb0] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11b2]	
	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-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-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 (2)

comment:1 by Eric Pettersen, 2 years ago

Cc: Tom Goddard Zach Pearson added
Component: Unassigned → Platform
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Networks: libbz2.so.1.0: cannot open shared object file: No such file or directory

comment:2 by Greg Couch, 2 years ago

Resolution: → wontfix
Status: assigned → closed

Not sure why libbz2.so.1.0 is being referred to. On CentOS 7, you should have /usr/lib64/libz2.so.1 from the bzip2-libs package. If not, "yum install bzip2-libs". You can fix this by adding a symbolic link in /opt/chimerax-1.3/lib to libbz2.so.1.0:

ln -s /usr/lib64/libbz2.so.1 /opt/chimerax-1.3/lib/libbz2.so.1.0

You might need to use sudo to give that command.

An aside, CentOS 7 is almost reached its end-of-life, and is already not supported by current versions of ChimeraX. You should upgrade your system ASAP and use a current version of ChimeraX. There have been *lots* of improvements.

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