Opened 3 years ago

Last modified 3 years ago

#7744 feedback defect

Maestro pose viewer file: KeyError: 'i_m_residue_number'

Reported by: afrance2@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Surface/Binding Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5.dev202206100131 (2022-06-10 01:31:06 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202206100131 (2022-06-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/amandaghilardi/Desktop/orai/prime/two/hORAI_knowledge_base/hORAI_knowledge_base-
> out.maegz

Chain information for hORAI_knowledge_base-out.maegz #1  
---  
Chain | Description  
A | No description available  
  
Opened hORAI_knowledge_base-out.maegz containing 1 structures (2171 atoms,
2199 bonds)  

> open /Users/amandaghilardi/Desktop/orai/prime/two/7kr5_a.pdb

7kr5_a.pdb title:  
Cryo-em structure of the crac channel orai In an open conformation; H206A
gain-of-function mutation In complex with an antibody [more info...]  
  
Chain information for 7kr5_a.pdb #2  
---  
Chain | Description | UniProt  
A | protein ORAI | CRCM1_DROME  
  
Non-standard residues in 7kr5_a.pdb #2  
---  
CA — calcium ion  
  

> matchmaker #1 to #2

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 7kr5_a.pdb, chain A (#2) with hORAI_knowledge_base-out.maegz, chain
A (#1), sequence alignment score = 115.4  
RMSD between 122 pruned atom pairs is 0.196 angstroms; (across all 127 pairs:
1.539)  
  

> matchmaker #1 to #2

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 7kr5_a.pdb, chain A (#2) with hORAI_knowledge_base-out.maegz, chain
A (#1), sequence alignment score = 115.4  
RMSD between 122 pruned atom pairs is 0.196 angstroms; (across all 127 pairs:
1.539)  
  

> ui tool show "Blast Protein"

> ui tool show AlphaFold

> alphafold match #1

No AlphaFold model with similar sequence for chain A  

Opened 0 AlphaFold model  

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> alphafold match
> MHPEPAPPPSRSSPELPPSGGSTTSGSRRSRRRSGDGEPPGAPPPPPSAVTYPDWIGQSYSEVMSLNEHSMQALSWRKLYLSRAKLKASSRTSALLSGFAMVAMVEVQLDADHDYPPGLLIAFSACTTVLVAVHLFALMISTCILPNIEAVSNVHNLNSVKESPHERMHRHIELAWAFSTVIGTLLFLAEVVLLCWVKFLPLKKQPGQPRPTSKPPASGAAANVSTSGITPGQAAAIASTTIMVPFGLIFIVFAVHFYRSLVSHKTDRQFQELNELAEFARLQDQLDHRGDHPLTPGSHYA

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
1 AlphaFold model found using sequence similarity searches: Q96D31 (1
sequences)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
CRCM1_HUMAN | MHPEP...GSHYA | 100.0 | 100.0  
Opened 1 AlphaFold model  

> hide #!2 models

> hide #1 models

> matchmaker #3 to #2

| 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 7kr5_a.pdb, chain A (#2) with AlphaFold CRCM1_HUMAN, chain A (#3),
sequence alignment score = 444.6  
RMSD between 116 pruned atom pairs is 0.782 angstroms; (across all 127 pairs:
1.815)  
  

> show #!2 models

> view

> hide #!2 models

> show #!2 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #!2 models

> show #!2 models

> close #1

> close #2

> save /Users/amandaghilardi/Desktop/orai/model_alpha.pdb relModel #3

> close session

> open /Users/amandaghilardi/Desktop/orai/alpha/model_alpha.pdb

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

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:1

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

> select /A:1-301

2302 atoms, 2370 bonds, 301 residues, 1 model selected  

> open /Users/amandaghilardi/Desktop/orai/modeller/two/orai.B99990001.pdb

Chain information for orai.B99990001.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> view

> open /Users/amandaghilardi/Desktop/orai/modeller/two/7kr5_a.pdb

7kr5_a.pdb title:  
Cryo-em structure of the crac channel orai In an open conformation; H206A
gain-of-function mutation In complex with an antibody [more info...]  
  
Chain information for 7kr5_a.pdb #3  
---  
Chain | Description | UniProt  
A | protein ORAI | CRCM1_DROME  
  
Non-standard residues in 7kr5_a.pdb #3  
---  
CA — calcium ion  
  

> matchmaker #2 to #3

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 7kr5_a.pdb, chain A (#3) with orai.B99990001.pdb, chain A (#2),
sequence alignment score = 443  
RMSD between 117 pruned atom pairs is 0.498 angstroms; (across all 127 pairs:
3.702)  
  

> open /Users/amandaghilardi/Desktop/orai/modeller/two/orai.B99990017.pdb

Chain information for orai.B99990017.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #2 models

> matchmaker #4 to #3

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 7kr5_a.pdb, chain A (#3) with orai.B99990017.pdb, chain A (#4),
sequence alignment score = 453.8  
RMSD between 115 pruned atom pairs is 0.525 angstroms; (across all 127 pairs:
4.099)  
  

> open /Users/amandaghilardi/Desktop/orai/modeller/multimer/orai.B99990001.pdb

Chain information for orai.B99990001.pdb #5  
---  
Chain | Description  
A B C D E F | No description available  
  

> hide #4 models

> hide #!3 models

> hide #5 atoms

> show #5 cartoons

> open
> /Users/amandaghilardi/Desktop/orai/prime/two/hORAI_hexamer_prepared/hORAI_hexamer_prepared-
> out.maegz

Chain information for hORAI_hexamer_prepared-out.maegz #6  
---  
Chain | Description  
A B C D E F | No description available  
  
Opened hORAI_hexamer_prepared-out.maegz containing 1 structures (11945 atoms,
12089 bonds)  

> hide #5 models

> hide #6 cartoons

> hide #6 atoms

> hide #6 cartoons

> show #6 cartoons

> open /Users/amandaghilardi/Desktop/orai/modeller/7kr5_orai.pdb

7kr5_orai.pdb title:  
Cryo-em structure of the crac channel orai In an open conformation; H206A
gain-of-function mutation In complex with an antibody [more info...]  
  
Chain information for 7kr5_orai.pdb #7  
---  
Chain | Description | UniProt  
A B C D E F | protein ORAI | CRCM1_DROME  
  
Non-standard residues in 7kr5_orai.pdb #7  
---  
CA — calcium ion  
  

> hide #6#!7 atoms

> show #6#!7 cartoons

> matchmaker #6 to #7

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 7kr5_orai.pdb, chain B (#7) with hORAI_hexamer_prepared-out.maegz,
chain B (#6), sequence alignment score = 131.8  
RMSD between 123 pruned atom pairs is 0.020 angstroms; (across all 127 pairs:
0.837)  
  

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #6 models

> show #6 models

> hide #!7 models

> select #6/A

1992 atoms, 2016 bonds, 127 residues, 1 model selected  

> select ~sel

37293 atoms, 38191 bonds, 7 pseudobonds, 4235 residues, 9 models selected  

> delete atoms (#6 & sel)

> delete bonds (#6 & sel)

> show #!3 models

> open /Users/amandaghilardi/Desktop/orai/modeller/multimer/align.ali

Summary of feedback from opening
/Users/amandaghilardi/Desktop/orai/modeller/multimer/align.ali  
---  
notes | Alignment identifier is align.ali  
Associated model_alpha.pdb chain A to orai with 0 mismatches  
Associated orai.B99990001.pdb chain A to orai with 0 mismatches  
Associated 7kr5_a.pdb chain A to 7kr5 with 0 mismatches  
Associated orai.B99990017.pdb chain A to orai with 0 mismatches  
Associated orai.B99990001.pdb chain A to orai with 0 mismatches  
Associated orai.B99990001.pdb chain B to orai with 0 mismatches  
Associated orai.B99990001.pdb chain C to orai with 0 mismatches  
Associated orai.B99990001.pdb chain D to orai with 0 mismatches  
Associated orai.B99990001.pdb chain E to orai with 0 mismatches  
1 messages similar to the above omitted  
Associated 7kr5_orai.pdb chain A to 7kr5 with 0 mismatches  
Associated 7kr5_orai.pdb chain B to 7kr5 with 0 mismatches  
Associated 7kr5_orai.pdb chain C to 7kr5 with 0 mismatches  
Associated 7kr5_orai.pdb chain D to 7kr5 with 0 mismatches  
Associated 7kr5_orai.pdb chain E to 7kr5 with 0 mismatches  
1 messages similar to the above omitted  
Showing conservation header ("seq_conservation" residue attribute) for
alignment align.ali  
  
Opened 2 sequences from align.ali  

> open /Users/amandaghilardi/Desktop/orai/Glide/test_7kr5/glide-
> dock_SP_el-19/glide-dock_SP_el-19_pv.maegz

Chain information for glide-dock_SP_el-19_pv.maegz  
---  
Chain | Description  
8.1/A 8.1/B 8.1/C 8.1/D 8.1/E 8.1/F | No description available  
  
Opened glide-dock_SP_el-19_pv.maegz containing 2 structures (12144 atoms,
12296 bonds)  

> open
> /Users/amandaghilardi/Desktop/orai/prime/two/hORAI_hexamer_prepared/hORAI_hexamer_prepared-
> out.maegz

Chain information for hORAI_hexamer_prepared-out.maegz #9  
---  
Chain | Description  
A B C D E F | No description available  
  
Opened hORAI_hexamer_prepared-out.maegz containing 1 structures (11945 atoms,
12089 bonds)  

> matchmaker #9 to #8

Specify a single 'to' model only  

> matchmaker #9 to #8.1

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 glide-dock_SP_el-19_pv.maegz, chain B (#8.1) with
hORAI_hexamer_prepared-out.maegz, chain B (#9), sequence alignment score =
115.7  
RMSD between 123 pruned atom pairs is 0.020 angstroms; (across all 127 pairs:
0.837)  
  

> hide sel & #!3 atoms

[Repeated 2 time(s)]

> show sel & #!3 atoms

> hide sel & #!3 atoms

[Repeated 1 time(s)]

> style sel & #!3 stick

Changed 948 atom styles  

> style sel & #!3 stick

Changed 948 atom styles  

> hide #6 models

> hide #!3 models

> style #9#8.1-2 stick

Changed 24089 atom styles  

> hide #9#8.1-2 atoms

> show #9#8.1-2 cartoons

> show #8.2

> select #8.2

38 atoms, 41 bonds, 1 residue, 1 model selected  

> select sel :< 5

1029 atoms, 993 bonds, 97 residues, 9 models selected  

> show sel

> hide ribbons

> select clear

> hide #!8 models

> show #!8 models

> hide #8.1 models

> show #8.1 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> open /Users/amandaghilardi/Desktop/orai/modeller/multimer/orai.B99990001.pdb

Chain information for orai.B99990001.pdb #10  
---  
Chain | Description  
A B C D E F | No description available  
  

> hide #!8 models

> hide #8.2 models

> hide #8.1 models

> hide #9 models

> hide #10 atoms

> show #10 cartoons

> show #9 models

> hide #9 models

> show #9 models

> hide protein

> show ribbons

> matchmaker #10 to #9

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 hORAI_hexamer_prepared-out.maegz, chain B (#9) with
orai.B99990001.pdb, chain B (#10), sequence alignment score = 75.6  
RMSD between 35 pruned atom pairs is 1.213 angstroms; (across all 127 pairs:
5.088)  
  

> select #10/A

2302 atoms, 2370 bonds, 301 residues, 1 model selected  

> select ~sel

64931 atoms, 66369 bonds, 7 pseudobonds, 6758 residues, 14 models selected  

> delete atoms (#9-10 & sel)

> delete bonds (#9-10 & sel)

> show #6 models

> matchmaker #10 to #6

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 hORAI_hexamer_prepared-out.maegz, chain A (#6) with
orai.B99990001.pdb, chain A (#10), sequence alignment score = 67  
RMSD between 36 pruned atom pairs is 1.010 angstroms; (across all 127 pairs:
4.505)  
  

> color #6 #7cee68 transparency 0

> select clear

> show protein

> style #6,10 stick

Changed 4294 atom styles  

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> open "/Users/amandaghilardi/Desktop/orai/Vina/ae-19/7kr5 copy.pdb"

7kr5 copy.pdb title:  
Cryo-em structure of the crac channel orai In an open conformation; H206A
gain-of-function mutation In complex with an antibody [more info...]  
  
Chain information for 7kr5 copy.pdb #9  
---  
Chain | Description | UniProt  
A B C D E F | protein ORAI | CRCM1_DROME  
H | 19B5 fab heavy chain |  
L N P | 19B5 fab light chain |  
M | 19B5 fab heavy chain |  
O | 19B5 fab heavy chain |  
  
Non-standard residues in 7kr5 copy.pdb #9  
---  
CA — calcium ion  
  

> hide #6 models

> hide #!9 models

> show #!9 models

> hide #10 models

> open /Users/amandaghilardi/Desktop/orai/Vina/ae-19/AE-19.pdb

AE-19.pdb title:  
AE-19 [more info...]  
  

> hide #!9 models

> view

> close session

> open /Users/amandaghilardi/Desktop/orai/Glide/test_7kr5/glide-
> dock_SP_7kr5/glide-dock_SP_7kr5_pv.maegz

Chain information for glide-dock_SP_7kr5_pv.maegz  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C 1.1/D 1.1/E 1.1/F | No description available  
  
Opened glide-dock_SP_7kr5_pv.maegz containing 2 structures (12368 atoms, 12535
bonds)  

> hide atoms

> show cartoons

> hide atoms

> show atoms

> hide protein

> open /Users/amandaghilardi/Desktop/orai/Glide/glide-dock_hORAI/glide-
> dock_hORAI_pv.maegz

Traceback (most recent call last):  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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 "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/__init__.py", line 16, in open  
return open_mae(session, path, file_name, True, True)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 12, in open_mae  
p = MaestroParser(session, stream, file_name, auto_style, atomic)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 62, in __init__  
s = self._make_structure(block)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
KeyError: 'i_m_residue_number'  
  

Populating font family aliases took 291 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

KeyError: 'i_m_residue_number'  
  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
  
See log for complete Python traceback.  
  

> open /Users/amandaghilardi/Desktop/orai/Glide/glide-dock_hORAI/glide-
> dock_hORAI_pv.maegz

Traceback (most recent call last):  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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 "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/__init__.py", line 16, in open  
return open_mae(session, path, file_name, True, True)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 12, in open_mae  
p = MaestroParser(session, stream, file_name, auto_style, atomic)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 62, in __init__  
s = self._make_structure(block)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
KeyError: 'i_m_residue_number'  
  
KeyError: 'i_m_residue_number'  
  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
  
See log for complete Python traceback.  
  

> open /Users/amandaghilardi/Desktop/orai/Glide/glide-
> dock_hORAI_2_29LIGANDS/glide-dock_hORAI_2_29LIGANDS_pv.maegz

Traceback (most recent call last):  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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 "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/__init__.py", line 16, in open  
return open_mae(session, path, file_name, True, True)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 12, in open_mae  
p = MaestroParser(session, stream, file_name, auto_style, atomic)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 62, in __init__  
s = self._make_structure(block)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
KeyError: 'i_m_residue_number'  
  
KeyError: 'i_m_residue_number'  
  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
  
See log for complete Python traceback.  
  

> open /Users/amandaghilardi/Desktop/orai/Glide/glide-
> dock_hORAI_2_29LIGANDS/glide-dock_hORAI_2_29LIGANDS.maegz

Traceback (most recent call last):  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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 "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/__init__.py", line 16, in open  
return open_mae(session, path, file_name, True, True)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 12, in open_mae  
p = MaestroParser(session, stream, file_name, auto_style, atomic)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 62, in __init__  
s = self._make_structure(block)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
KeyError: 'i_m_residue_number'  
  
KeyError: 'i_m_residue_number'  
  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
  
See log for complete Python traceback.  
  

> open /Users/amandaghilardi/Desktop/orai/Glide/glide-
> grid_sp_hORAI_20-el114/glide-grid_sp_hORAI_20-el114.maegz

Chain information for glide-grid_sp_hORAI_20-el114.maegz #2  
---  
Chain | Description  
A B C D E F | No description available  
  
Opened glide-grid_sp_hORAI_20-el114.maegz containing 1 structures (11945
atoms, 12089 bonds)  

> hide atoms

> show cartoons

> color #2 #87cfeb transparency 0

[Repeated 1 time(s)]

> hide #2 models

> show #2 models

> hide #!1.2 models

> show #!1.2 models

> matchmaker #2 to #1

Specify a single 'to' model only  

> matchmaker #2 to #1.2

Specify a single 'to' model only  

> matchmaker #2 to #1.1

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 glide-dock_SP_7kr5_pv.maegz, chain B (#1.1) with glide-
grid_sp_hORAI_20-el114.maegz, chain B (#2), sequence alignment score = 115.7  
RMSD between 123 pruned atom pairs is 0.020 angstroms; (across all 127 pairs:
0.837)  
  

> hide #!1.2 models

> show #!1.2 models

> hide #1.1 models

> show #1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> view

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> open
> /Users/amandaghilardi/Desktop/orai/Glide/prime_mmgbsa_sp_hORAI_1/prime_mmgbsa_sp_hORAI_1-out.maegz

Traceback (most recent call last):  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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 "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/__init__.py", line 16, in open  
return open_mae(session, path, file_name, True, True)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 12, in open_mae  
p = MaestroParser(session, stream, file_name, auto_style, atomic)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 62, in __init__  
s = self._make_structure(block)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
KeyError: 'i_m_residue_number'  
  
KeyError: 'i_m_residue_number'  
  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
  
See log for complete Python traceback.  
  

> open
> /Users/amandaghilardi/Desktop/orai/Glide/prime_mmgbsa_sp_hORAI_1/prime_mmgbsa_sp_hORAI_1-out.maegz

Traceback (most recent call last):  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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 "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/__init__.py", line 16, in open  
return open_mae(session, path, file_name, True, True)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 12, in open_mae  
p = MaestroParser(session, stream, file_name, auto_style, atomic)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 62, in __init__  
s = self._make_structure(block)  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
KeyError: 'i_m_residue_number'  
  
KeyError: 'i_m_residue_number'  
  
File "/Users/amandaghilardi/Desktop/md-intro-
tutorial/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/maestro/io.py", line 108, in _make_structure  
res_seq = attrs["i_m_residue_number"]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 8-Core Intel Core i7
      Processor Speed: 3.8 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0)
      OS Loader Version: 540.40.4~45

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 9 days 6:12

Graphics/Displays:

    AMD Radeon Pro 5500 XT:

      Chipset Model: AMD Radeon Pro 5500 XT
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0041
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XT-011
      Option ROM Version: 113-D322A1XT-011
      EFI Driver Version: 01.01.231
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.7.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.2
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.5.dev202206100131
    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: 1.1
    ChimeraX-DistMonitor: 1.1.6
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.2
    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: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6.2
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.20.4
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.12.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Maestro pose viewer file: KeyError: 'i_m_residue_number'

comment:2 by Eric Pettersen, 3 years ago

Status: accepted → feedback

Hi Amanda,

Thanks for reporting this problem. I would need a copy of your Glide/prime_mmgbsa_sp_hORAI_1/prime_mmgbsa_sp_hORAI_1-out.maegz file in order to try to fix it. You could send it to me directly at pett@… if you need it to remain private.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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