Old bundle installed

[fred.mast@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202109290359 (2021-09-29 03:59:25 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202109290359 (2021-09-29)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/fredmast/Dropbox/chimerax files/RBD_similarity/3kbh.cif"

3kbh.cif title:  
Crystal structure of NL63 respiratory coronavirus receptor-binding domain
complexed with its human receptor [more info...]  
  
Chain information for 3kbh.cif #1  
---  
Chain | Description | UniProt  
A B C D | Angiotensin-converting enzyme 2 | ACE2_HUMAN  
E F G H | Spike glycoprotein | SPIKE_CVHNL  
  
Non-standard residues in 3kbh.cif #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  
3kbh.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> ui tool show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  

> ui tool show Updates

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application Support/ChimeraX/1.3/site-
packages  
sysconfig: /Users/fredmast/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application Support/ChimeraX/1.3/site-
packages  
sysconfig: /Users/fredmast/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application
Support/ChimeraX/include/python3.9/MolecularDynamicsViewer  
sysconfig: /Users/fredmast/Library/Python/3.9/include/MolecularDynamicsViewer  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/fredmast/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application Support/ChimeraX  
sysconfig: /Users/fredmast/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-UI  
sysconfig: /Users/fredmast/Library/Python/3.9/include/ChimeraX-UI  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application
Support/ChimeraX/include/python3.9/ChimeraX-PDBImages  
sysconfig: /Users/fredmast/Library/Python/3.9/include/ChimeraX-PDBImages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /Users/fredmast/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/fredmast/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting MolecularDynamicsViewer==1.2  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/moleculardynamicsviewer/releases/1.2/MolecularDynamicsViewer-1.2-py3-none-
any.whl (6.3 kB)  
Collecting ChimeraX-PDBImages==1.1  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxpdbimages/releases/1.1/ChimeraX_PDBImages-1.1-py3-none-
any.whl (4.3 kB)  
Collecting ChimeraX-UI==1.2.1  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxui/releases/1.2.1/ChimeraX_UI-1.2.1-py3-none-
any.whl (1.1 MB)  
Installing collected packages: MolecularDynamicsViewer, ChimeraX-UI, ChimeraX-
PDBImages  
Successfully installed ChimeraX-PDBImages-1.1 ChimeraX-UI-1.2.1
MolecularDynamicsViewer-1.2  
\---  

Successfully installed ChimeraX-PDBImages-1.1 ChimeraX-UI-1.2.1
MolecularDynamicsViewer-1.2  
Installed ChimeraX-PDBImages (1.1)  
Installed ChimeraX-UI (1.2.1)  
Installed MolecularDynamicsViewer (1.2)  

> toolshed show

> log metadata #1

Metadata for 3kbh.cif #1  
---  
Title | Crystal structure of NL63 respiratory coronavirus receptor-binding
domain complexed with its human receptor  
Citation | Wu, K., Li, W., Peng, G., Li, F. (2009). Crystal structure of NL63
respiratory coronavirus receptor-binding domain complexed with its human
receptor. Proc.Natl.Acad.Sci.USA, 106, 19970-19974. PMID: 19901337. DOI:
10.1073/pnas.0908837106  
Non-standard residue | NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
Gene sources | Human coronavirus NL63  
Homo sapiens (human)  
Experimental method | X-ray diffraction  
Resolution | 3.3Å  
  
> close session

> open /Users/fredmast/Downloads/7lwm.cif

7lwm.cif title:  
Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the
1-RBD up conformation [more info...]  
  
Chain information for 7lwm.cif #1  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2  
  
Non-standard residues in 7lwm.cif #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open /Users/fredmast/Downloads/6xm0.cif

6xm0.cif title:  
Consensus structure of SARS-CoV-2 spike at pH 5.5 [more info...]  
  
Chain information for 6xm0.cif #2  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2  
  
Non-standard residues in 6xm0.cif #2  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> close session

> open /Users/fredmast/Downloads/6xm0.cif format mmcif

6xm0.cif title:  
Consensus structure of SARS-CoV-2 spike at pH 5.5 [more info...]  
  
Chain information for 6xm0.cif #1  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2  
  
Non-standard residues in 6xm0.cif #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> close session

> open /Users/fredmast/Downloads/7nd9.cif

Summary of feedback from opening /Users/fredmast/Downloads/7nd9.cif  
---  
note | Fetching CCD FUC from http://ligand-expo.rcsb.org/reports/F/FUC/FUC.cif  
  
7nd9.cif title:  
EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with
COVOX-253H55L Fab [more info...]  
  
Chain information for 7nd9.cif #1  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2  
H | COVOX-253H55L Fab heavy chain |  
L | COVOX-253H55L Fab light chain |  
  
Non-standard residues in 7nd9.cif #1  
---  
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select /H

1633 atoms, 1674 bonds, 1 pseudobond, 219 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> select /L

1639 atoms, 1678 bonds, 214 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> select /A/B/C

23746 atoms, 24341 bonds, 23 pseudobonds, 3076 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> hide sel surfaces

> select

27336 atoms, 28034 bonds, 24 pseudobonds, 3532 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> select /A/B/C

23746 atoms, 24341 bonds, 23 pseudobonds, 3076 residues, 2 models selected  

> show sel cartoons

> ui tool show "Color Actions"

> color sel antique white

> color sel light yellow

> lighting flat

> lighting soft

> hide #!1 models

> show #!1 models

> select #1

27336 atoms, 28034 bonds, 24 pseudobonds, 3532 residues, 2 models selected  

> ~select #1

Nothing selected  

> set bgColor white

> open
> /Users/fredmast/Dropbox/proteomes_fasta/spike_combined_beta_subset.prank.best.fas

Unrecognized file suffix '.fas'  

> open
> /Users/fredmast/Dropbox/proteomes_fasta/spike_combined_beta_subset_PRANKaligned.fa

Summary of feedback from opening
/Users/fredmast/Dropbox/proteomes_fasta/spike_combined_beta_subset_PRANKaligned.fa  
---  
notes | Alignment identifier is spike_combined_beta_subset_PRANKaligned.fa  
Associated 7nd9.cif chain A to Sarbecovirus 1b SARS-CoV-2_Wuhan-Hu-1 with 68
mismatches  
Associated 7nd9.cif chain B to Sarbecovirus 1b SARS-CoV-2_Wuhan-Hu-1 with 68
mismatches  
Associated 7nd9.cif chain C to Sarbecovirus 1b SARS-CoV-2_Wuhan-Hu-1 with 68
mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment spike_combined_beta_subset_PRANKaligned.fa  
  
Opened 9 sequences from spike_combined_beta_subset_PRANKaligned.fa  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /C

Alignment identifier is 1  

> ui tool show "Molecular Dynamics Viewer"

Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

> surface cap false

> sequence header spike_combined_beta_subset_PRANKaligned.fa consensus show

Showing consensus header ("seq_consensus" residue attribute) for alignment
spike_combined_beta_subset_PRANKaligned.fa  

> select /A:589 /B:589 /C:589

21 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:589-590

39 atoms, 39 bonds, 6 residues, 1 model selected  

> select /A-C:589-600

240 atoms, 246 bonds, 36 residues, 1 model selected  

> select /A-C:484-485

39 atoms, 36 bonds, 6 residues, 1 model selected  

> select /A-C:484-510

666 atoms, 693 bonds, 81 residues, 1 model selected  

> select /A-C:488

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select /A-C:488-509

549 atoms, 573 bonds, 66 residues, 1 model selected  

> ui tool show "Color Actions"

> select /A-C:510

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select /A-C:510-514

105 atoms, 102 bonds, 15 residues, 1 model selected  

> color sel red

> select /A-C:515

33 atoms, 33 bonds, 3 residues, 1 model selected  

> select /A-C:515

33 atoms, 33 bonds, 3 residues, 1 model selected  

> select /A-C:527

21 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:527

21 atoms, 21 bonds, 3 residues, 1 model selected  

> color sel red

> select /A-C:538

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select /A-C:538-540

63 atoms, 60 bonds, 9 residues, 1 model selected  

> color sel red

> select /A-C:545

12 atoms, 9 bonds, 3 residues, 1 model selected  

> select /A-C:545-546

36 atoms, 33 bonds, 6 residues, 1 model selected  

> color sel red

> select /A-C:548

12 atoms, 9 bonds, 3 residues, 1 model selected  

> select /A-C:548-551

66 atoms, 63 bonds, 12 residues, 1 model selected  

> color sel red

[Repeated 6 time(s)]

> select /A-C:714

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:714-725

276 atoms, 279 bonds, 36 residues, 1 model selected  

> color sel red

> select /A-C:730-731

42 atoms, 39 bonds, 6 residues, 1 model selected  

> select /A-C:730-734

111 atoms, 108 bonds, 15 residues, 1 model selected  

> color sel red

> select /A/B/C

23746 atoms, 24341 bonds, 23 pseudobonds, 3076 residues, 2 models selected  

> color (#!1 & sel) #bcffa6ff

> color (#!1 & sel) #bbffa6ff

> color (#!1 & sel) #93ff38ff

> color (#!1 & sel) #f1ff15ff

> color (#!1 & sel) #fbff1aff

> color (#!1 & sel) #fcff1cff

> color (#!1 & sel) #fff730ff

> color (#!1 & sel) #ffe83dff

> color (#!1 & sel) #ffd945ff

[Repeated 1 time(s)]

> color (#!1 & sel) #ff8ac6ff

[Repeated 1 time(s)]

> color (#!1 & sel) #c574ffff

[Repeated 1 time(s)]

> color (#!1 & sel) #3781ffff

> color (#!1 & sel) #3782ffff

> color (#!1 & sel) #28ffd2ff

[Repeated 1 time(s)]

> color (#!1 & sel) #a5fffaff

[Repeated 1 time(s)]

> ui tool show "Surface Color"

> ui tool show "Color Actions"

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> ui tool show "Color Actions"

> ui tool show "Modeller Comparative"

<QNSWindow: 0x7ff2da769300; contentView=<QNSView: 0x7ff2da769040;
QCocoaWindow(0x60000035a680, window=QWidgetWindow(0x600001e4cf60,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  
<QNSWindow: 0x7ff3217ee680; contentView=<QNSView: 0x7ff2e2ad0b10;
QCocoaWindow(0x600000303b20, window=QWidgetWindow(0x600001e77600,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  

> toolshed show

> ui tool show "Color Zone"

> volume style surface

No volumes specified  

> volume style image

No volumes specified  
Alignment identifier is 2  
Alignment identifier is 3  

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A LYS 129  
/A PHE 135  
/A CYS 136  
/A ASN 188  
/A GLU 191  
/A ASN 196  
/A ARG 214  
/A ARG 237  
/A GLN 239  
/A LEU 242  
/A GLU 281  
/A GLU 298  
/A ASP 389  
/A LYS 528  
/A GLU 554  
/A LYS 558  
/A ASP 568  
/A ASP 571  
/A ASP 614  
/A GLU 619  
/A ARG 634  
/A ARG 646  
/A GLU 661  
/A ASP 745  
/A LYS 786  
/A LYS 811  
/A LYS 814  
/A LYS 1045  
/A GLU 1092  
/A GLU 1144  
/A ASP 1146  
/B ASN 81  
/B GLU 96  
/B LYS 97  
/B ASN 125  
/B GLU 132  
/B GLN 134  
/B CYS 136  
/B ASN 137  
/B ASP 138  
/B GLU 156  
/B ARG 158  
/B ASN 188  
/B ILE 210  
/B ASP 215  
/B GLN 218  
/B GLU 309  
/B GLU 324  
/B THR 333  
/B LYS 528  
/B LYS 529  
/B LYS 537  
/B GLU 554  
/B LYS 558  
/B GLU 583  
/B ARG 646  
/B GLU 661  
/B GLU 748  
/B LYS 786  
/B ILE 794  
/B ASP 796  
/B LYS 811  
/B LYS 814  
/B ILE 844  
/B ARG 847  
/B LYS 1045  
/B GLU 1092  
/B GLN 1142  
/B LEU 1145  
/B ASP 1146  
/C LYS 41  
/C SER 46  
/C ASN 81  
/C ASP 88  
/C LYS 97  
/C LEU 110  
/C SER 112  
/C LYS 113  
/C GLN 115  
/C ASN 125  
/C LYS 129  
/C GLU 132  
/C GLN 134  
/C CYS 136  
/C ASN 137  
/C ASP 138  
/C GLU 169  
/C SER 172  
/C GLU 191  
/C ASP 198  
/C ASN 211  
/C VAL 213  
/C ARG 214  
/C ASP 215  
/C GLN 239  
/C LEU 242  
/C GLU 281  
/C GLU 324  
/C LYS 458  
/C GLU 661  
/C ASP 745  
/C GLU 748  
/C LYS 786  
/C ILE 794  
/C LYS 811  
/C LYS 814  
/C ASP 830  
/C GLU 868  
/C SER 940  
/C ASP 985  
/C GLU 988  
/C LYS 1045  
/C GLU 1092  
/C ASP 1146  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 7nd9.cif_A SES surface #1.2: minimum, -28.62, mean -1.53,
maximum 14.28  
Coulombic values for 7nd9.cif_B SES surface #1.3: minimum, -18.04, mean -1.81,
maximum 14.99  
Coulombic values for 7nd9.cif_C SES surface #1.4: minimum, -29.60, mean -1.38,
maximum 23.08  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color byattribute seq_conservation

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range 100 to 100  

> select ~::seq_conservation

3968 atoms, 4098 bonds, 1 pseudobond, 483 residues, 3 models selected  

> select clear

> color byattribute seq_conservation

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range 100 to 100  

> select
> /A:28-31,36-37,42-43,47-55,60-65,83-85,89-95,101-107,117-122,125-129,132-135,169-172,189-197,200-208,222-229,237-242,264-269,271-279,285-290,309-319,324-328,354-358,361-362,376-380,391-392,394-403,431-437,452-454,473-474,488-489,492-494,507-516,524-525,538-543,546-554,565-566,575-577,584-588,592-601,609-613,642-645,648-651,654-655,664-667,670-675,691-696,701-704,711-715,718-728,733-736,787-790,858-861,1047-1056,1059-1069,1072-1078,1081-1082,1086-1090,1094-1097,1102-1106,1109-1114,1120-1125,1133-1134/B:28-31,36-37,42-43,47-55,60-65,83-85,89-95,101-107,117-122,125-129,132-135,160-164,169-172,189-197,200-208,222-229,237-242,264-269,271-279,285-290,309-319,324-328,354-358,361-362,376-380,391-392,394-403,431-437,452-454,473-474,488-489,492-494,507-516,524-525,538-543,546-554,565-566,575-577,584-588,592-601,609-613,642-645,648-651,654-655,664-667,670-675,691-696,701-704,711-715,718-728,733-736,787-790,858-861,1047-1056,1059-1069,1072-1078,1081-1082,1086-1090,1094-1097,1102-1106,1109-1114,1120-1125,1133-1134/C:28-31,36-37,42-43,47-55,60-65,83-85,89-95,101-107,117-122,125-129,132-135,169-172,189-197,200-208,222-229,237-269,271-279,285-290,309-319,324-328,354-358,361-362,376-380,391-392,394-403,431-437,452-454,473-474,488-489,492-494,507-516,524-525,538-543,546-554,565-566,575-577,584-588,592-601,609-613,642-645,648-651,654-655,664-667,670-675,691-696,701-704,711-715,718-728,733-736,787-790,858-861,1047-1056,1059-1069,1072-1078,1081-1082,1086-1090,1094-1097,1102-1106,1109-1114,1120-1125,1133-1134

8171 atoms, 8232 bonds, 1 pseudobond, 1016 residues, 2 models selected  

> color byattribute seq_consensus

No known/registered attribute seq_consensus  

> color byattribute seq_consensus

No known/registered attribute seq_consensus  

> color byattribute seq_conservation

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range 100 to 100  

> color byattribute seq_conservation

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range 100 to 100  

> sequence associate /A spike_combined_beta_subset_PRANKaligned.fa:8

Disassociated 7nd9.cif chain A from Sarbecovirus 1b SARS-CoV-2_Wuhan-Hu-1  
Associated 7nd9.cif chain A to Merbecovirus MERS-CoV with 1031 mismatches
and/or gaps  

> sequence associate /B spike_combined_beta_subset_PRANKaligned.fa:8

Disassociated 7nd9.cif chain B from Sarbecovirus 1b SARS-CoV-2_Wuhan-Hu-1  
Associated 7nd9.cif chain B to Merbecovirus MERS-CoV with 1031 mismatches
and/or gaps  

> sequence associate /C spike_combined_beta_subset_PRANKaligned.fa:8

Disassociated 7nd9.cif chain C from Sarbecovirus 1b SARS-CoV-2_Wuhan-Hu-1  
Associated 7nd9.cif chain C to Merbecovirus MERS-CoV with 1031 mismatches
and/or gaps  

> color byattribute seq_conservation

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -1.98 to
100  

> sequence associate /A spike_combined_beta_subset_PRANKaligned.fa:3

Disassociated 7nd9.cif chain A from Merbecovirus MERS-CoV  
Associated 7nd9.cif chain A to Sarbecovirus 1a SARS-CoV-1_TOR2 with 348
mismatches and/or gaps  

> sequence associate /B spike_combined_beta_subset_PRANKaligned.fa:3

Disassociated 7nd9.cif chain B from Merbecovirus MERS-CoV  
Associated 7nd9.cif chain B to Sarbecovirus 1a SARS-CoV-1_TOR2 with 348
mismatches and/or gaps  

> sequence associate /C spike_combined_beta_subset_PRANKaligned.fa:3

Disassociated 7nd9.cif chain C from Merbecovirus MERS-CoV  
Associated 7nd9.cif chain C to Sarbecovirus 1a SARS-CoV-1_TOR2 with 348
mismatches and/or gaps  

> color byattribute seq_conservation

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor silver key true

> key cyan-white-maroon :-2.0 :0.5 :3.0 showTool true

> ui mousemode right "color key"

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> sequence associate /A spike_combined_beta_subset_PRANKaligned.fa:8

Disassociated 7nd9.cif chain A from Sarbecovirus 1a SARS-CoV-1_TOR2  
Associated 7nd9.cif chain A to Merbecovirus MERS-CoV with 1031 mismatches
and/or gaps  

> sequence associate /B spike_combined_beta_subset_PRANKaligned.fa:8

Disassociated 7nd9.cif chain B from Sarbecovirus 1a SARS-CoV-1_TOR2  
Associated 7nd9.cif chain B to Merbecovirus MERS-CoV with 1031 mismatches
and/or gaps  

> sequence associate /C spike_combined_beta_subset_PRANKaligned.fa:8

Disassociated 7nd9.cif chain C from Sarbecovirus 1a SARS-CoV-1_TOR2  
Associated 7nd9.cif chain C to Merbecovirus MERS-CoV with 1031 mismatches
and/or gaps  

> color byattribute seq_conservation palette cyanmaroon range -2,3
> noValueColor silver key true

> key cyan-white-maroon :-2.0 :0.5 :3.0 showTool true

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> key ylgn-3 :-2.0 :0.5 :3.0

> color byattribute seq_conservation palette ylgn-3 range -2,3 noValueColor
> silver key true

> key ylgn-3 :-2.0 :0.5 :3.0 showTool true

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> key lipophilicity :-2.0 :0.5 :3.0

> key accent-3 :-2.0 :0.5 :3.0

> key accent-3 :-2.0 :0 :3.0

> key accent-3 :-.0 :0 :3.0

> key accent-3 :-.03 :0 :3.0

> key accent-3 :-.0 :0 :3.0

> key accent-3 :-. :0 :3.0

> key accent-3 :- :0 :3.0

> key accent-3 :-3 :0 :3.0

> color byattribute seq_conservation palette accent-3 range -3,3 noValueColor
> silver key true

> key accent-3 :-3 :0 :3 showTool true

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> key cyan-white-maroon :-3 :0 :3

> color byattribute seq_conservation palette cyan-white-maroon range -3,3
> noValueColor silver key true

> key cyan-white-maroon :-3 :0 :3 showTool true

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> color byattribute seq_conservation palette cyan-white-maroon range -10,10
> noValueColor silver key true

> key cyan-white-maroon :-10 :0 :10 showTool true

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> color byattribute seq_conservation palette cyan-white-maroon range -1,1
> noValueColor silver key true

> key cyan-white-maroon :-1 :0 :1 showTool true

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -2.23 to
100  

> sequence associate /A spike_combined_beta_subset_PRANKaligned.fa:9

Disassociated 7nd9.cif chain A from Merbecovirus MERS-CoV  
Associated 7nd9.cif chain A to Embecovirus HCoV-OC43 with 1012 mismatches
and/or gaps  

> sequence associate /B spike_combined_beta_subset_PRANKaligned.fa:9

Disassociated 7nd9.cif chain B from Merbecovirus MERS-CoV  
Associated 7nd9.cif chain B to Embecovirus HCoV-OC43 with 1012 mismatches
and/or gaps  

> sequence associate /C spike_combined_beta_subset_PRANKaligned.fa:9

Disassociated 7nd9.cif chain C from Merbecovirus MERS-CoV  
Associated 7nd9.cif chain C to Embecovirus HCoV-OC43 with 1012 mismatches
and/or gaps  

> color byattribute seq_conservation palette cyan-white-maroon range -1,1
> noValueColor silver key true

> key cyan-white-maroon :-1 :0 :1 showTool true

27336 atoms, 3532 residues, 3 surfaces, atom seq_conservation range -1.98 to
100  

> windowsize 600 600

> windowsize 900 900

> windowsize 600 600

> close session

> ui mousemode right translate

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq-view/associations_tool.py", line 71, in _chain_changed  
self.tool_window.shown = False  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2095, in shown  
ui.main_window._tool_window_request_shown(self, shown)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1890, in _tool_window_request_shown  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.seq-view.tool.SequenceViewer object at 0x7ff2e12ae400>  
  
KeyError:  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1890, in _tool_window_request_shown  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.7.101
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 447.60.3.0.0
      OS Loader Version: 540.60.2~89
      SMC Version (system): 2.45f5

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 6:45

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AU-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.1
    ChimeraX-AtomicLibrary: 4.1.4
    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
    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: 2.1
    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.dev202109290359
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    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: 2.1.1
    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-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: 2.0.1
    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
    ChimeraX-ModelPanel: 1.2
    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: 1.7
    ChimeraX-PDB: 2.6.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    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: 2.4.4
    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
    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: 1.2.1
    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: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    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: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.2
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    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: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.1
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    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: 2.1.0
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Greg, this user (Fred Mast) was allowed to install a very old, obsolete version of the UI bundle into his ChimeraX. Why? This should definitely be disallowed. There are many bundles (e.g. ColorKey) that depend on more recent versions of UI.

Fred, try "toolshed uninstall UI" in your ChimeraX. If that doesn't succeed, you may need to remove the UI "manually". If that "toolshed" command fails, let us know and we can send further instructions.

[Fred.Mast@…]

Hi,
Thank-you for your fast response! The 'toolshed uninstall UI' command didn’t work and the program gave the following error:
 Unable to uninstall ChimeraX-UI because it is needed by other bundles: ChimeraX-Contacts, ChimeraX-Help, ChimeraX-SeqView, ChimeraX-Registration, ChimeraX-Clashes, ChimeraX-Shortcuts, ChimeraX-ModelPanel, ChimeraX-SwapAA, ChimeraX-Map, ChimeraX-CrystalContacts, ChimeraX-BondRot, ChimeraX-Tug, ChimeraX-ModelSeries, ChimeraX-BuildStructure, ChimeraX-Hbonds, ChimeraX-Toolbar, ChimeraX-FunctionKey, ChimeraX-Markers, ChimeraX-AltlocExplorer, ChimeraX-Alignments, ChimeraX-Log, ChimeraX-Modeller, ChimeraX-MedicalToolbar, ChimeraX-MapSeries, ChimeraX-BlastProtein, ChimeraX-UnitCell, ChimeraX-ShowSequences, ChimeraX-Label, ChimeraX-Mask, ChimeraX-ButtonPanel, ChimeraX-PickBlobs, ChimeraX-VolumeMenu, ChimeraX-SwapRes, ChimeraX-SideView, ChimeraX-ShowAttr, ChimeraX-ItemsInspection, ChimeraX-ResidueFit, ChimeraX-Nucleotides, ChimeraX-SelInspector, ChimeraX-BasicActions, ChimeraX-Zone, ChimeraX-StructMeasure, ChimeraX-Segger, ChimeraX-MapEraser, ChimeraX-OpenCommand, ChimeraX-ColorActions, ChimeraX-CageBuilder, ChimeraX-Shell, ChimeraX-ColorKey, ChimeraX-BugReporter, ChimeraX-CommandLine, ChimeraX-Meeting, ChimeraX-SaveCommand, ChimeraX-ViewDockX, and ChimeraX-FileHistory

Please send instructions for doing this manually.
Cheers,
Fred

Fred D. Mast, PhD
Senior Research Scientist | Center for Global Infectious Disease Research
Seattle Children's Research Institute

206-884-3189  OFFICE
206-229-6497  CELL
fred.mast@seattlechildrens.org

OFFICE   307 Westlake Ave N, Ste 500, Seattle, WA 98109
WWW     seattlechildrens.org/research

[Eric Pettersen]

Hi Fred,

Remove these folders:

/Users/fredmast/Library/Application Support/ChimeraX/1.3/site-packages/chimerax/ui
/Users/fredmast/Library/Application Support/ChimeraX/1.3/site-packages/ChimeraX_UI-1.2.1.dist-info

Then start/restart ChimeraX. Then use the command "toolshed list installed" and look for the UI bundle in the log output. The version number should be much higher than 1.2.1.

--Eric