error evaluating selector

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.3-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2bbv format mmcif fromDatabase pdb

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  

Chain information for 2bbv #1  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |  

Non-standard residues in 2bbv #1  
---  
CA \u2014 calcium ion  

2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  


> hide #!1 models

> show #!1 models

> open 2bbv format mmcif fromDatabase pdb

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  

Chain information for 2bbv #2  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |  

Non-standard residues in 2bbv #2  
---  
CA \u2014 calcium ion  

2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  


> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> select clear

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ui tool show "Selection Inspector"

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> show atoms

> open 2bbv format mmcif fromDatabase pdb

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  

Chain information for 2bbv #3  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |  

Non-standard residues in 2bbv #3  
---  
CA \u2014 calcium ion  

2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  


> close session

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> save /Users/lulahlyons/Desktop/image1.png supersample 3

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> open 2bbv format mmcif fromDatabase pdb

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  

Chain information for 2bbv #1  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |  

Non-standard residues in 2bbv #1  
---  
CA \u2014 calcium ion  

2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  


> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete all

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> show atoms

[Repeated 3 time(s)]

> hide atoms

[Repeated 1 time(s)]

> style stick

Changed 0 atom styles  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> open O00329

'O00329' has no suffix  

> open "Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta
> isoform" fromDatabase iupac format iupac

Web services failed to translate IUPAC name to SMILES string.  
For more information about the failure, go to
https://opsin.ch.cam.ac.uk/index.html and input the IUPAC name by hand.  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ~select

Nothing selected  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> show surfaces

[Repeated 1 time(s)]

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> select clear

[Repeated 15 time(s)]

> color bychain

> show atoms

[Repeated 1 time(s)]

> ui tool show "Selection Inspector"

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> set bgColor white

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Destroying pre-existing alignment with identifier PK3CD_HUMAN  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> open " O00329-1" fromDatabase uniprot format uniprot

Summary of feedback from opening O00329-1 fetched from uniprot  
---  
notes | UniProt identifier O00329-1 maps to entry O00329  
Alignment identifier is O00329-1  

Opened UniProt O00329-1  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> ~select

Nothing selected  

> open " O00329-1" format uniprot fromDatabase uniprot

Summary of feedback from opening O00329-1 fetched from uniprot  
---  
notes | UniProt identifier O00329-1 maps to entry O00329  
Destroying pre-existing alignment with identifier O00329-1  
Alignment identifier is O00329-1  

Opened UniProt O00329-1  

> select clear

[Repeated 9 time(s)]

> ui mousemode right select

> open " O00329-1" format uniprot fromDatabase uniprot

Summary of feedback from opening O00329-1 fetched from uniprot  
---  
notes | UniProt identifier O00329-1 maps to entry O00329  
Destroying pre-existing alignment with identifier O00329-1  
Alignment identifier is O00329-1  

Opened UniProt O00329-1  

> open " O00329-1" format uniprot fromDatabase uniprot

Summary of feedback from opening O00329-1 fetched from uniprot  
---  
notes | UniProt identifier O00329-1 maps to entry O00329  
Destroying pre-existing alignment with identifier O00329-1  
Alignment identifier is O00329-1  

Opened UniProt O00329-1  

> ~select

Nothing selected  

> show cartoons

> show surfaces

> select clear

[Repeated 7 time(s)]

> open PK3CD_HUMAN format uniprot fromDatabase uniprot

Summary of feedback from opening PK3CD_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PK3CD_HUMAN maps to entry O00329  
Alignment identifier is PK3CD_HUMAN  

Opened UniProt PK3CD_HUMAN  

> ~select

Nothing selected  

> ui tool show "Show Sequence Viewer"

> select clear

> open AF-O00329-F1 fromDatabase alphafold format mmcif

UniProt identifiers must be 6 or 10 characters long, got "AF-O00329-F1"  

> open O00329-F1 fromDatabase alphafold format mmcif

UniProt identifiers must be 6 or 10 characters long, got "O00329-F1"  

> open /Users/lulahlyons/Downloads/AF-O00329-F1-model_v4.pdb

AF-O00329-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate
3-kinase catalytic subunit \u03b4 isoform (O00329) [more info...]  

Chain information for AF-O00329-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit \u03b4 isoform
| PK3CD_HUMAN 1-1044  

Associated AF-O00329-F1-model_v4.pdb chain A to O00329-1 with 0 mismatches  
Associated AF-O00329-F1-model_v4.pdb chain A to PK3CD_HUMAN with 0 mismatches  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 8396 atom styles  

> lighting full

> volume style surface

No volumes specified  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> color bynucleotide

> color byhetero

> rainbow

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "AF-O00329-F1-model_v4.pdb_A SES surface": minimum
-29.14, mean -4.734, maximum 24.33  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bychain

[Repeated 1 time(s)]

> color bypolymer

> rainbow

> style ball

Changed 8396 atom styles  

> style ball

Changed 8396 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> show surfaces

> show cartoons

> show atoms

[Repeated 1 time(s)]

> style stick

Changed 8396 atom styles  

> style ball

Changed 8396 atom styles  

> coulombic

Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color bfactor

8396 atoms, 1044 residues, 1 surfaces, atom bfactor range 31.7 to 98.8  

> rainbow

> color bynucleotide

> style ball

Changed 8396 atom styles  

> nucleotides ladder

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> lighting simple

> lighting soft

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 8396 atom styles  

> style sphere

Changed 8396 atom styles  

> style ball

Changed 8396 atom styles  

> rainbow

> graphics silhouettes true

> graphics silhouettes false

> volume style mesh

No volumes specified  

> transparency 50

> sequence chain /A

Alignment identifier is 1/A  

> select /A:451

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

> select /A:451-467

126 atoms, 127 bonds, 17 residues, 1 model selected  

> select
> /A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select /A:451-467

126 atoms, 127 bonds, 17 residues, 1 model selected  

> select
> /A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select /A:451-467

126 atoms, 127 bonds, 17 residues, 1 model selected  

> select
> /A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> color sel byhetero

[Repeated 1 time(s)]

> color sel bychain

> color sel bypolymer

[Repeated 1 time(s)]

> rainbow sel

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> ~hbonds

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> volume hide

No volumes specified  

> transparency sel 0

[Repeated 2 time(s)]

> select
> /A:19-25,31-37,68-73,79-82,98-103,189-196,202-208,239-243,273-278,324-331,340-348,373-376,389-399,413-424,435-440,470-475,759-765,772-780,815-819,822-826,831-833,899-902,907-909

1182 atoms, 1185 bonds, 148 residues, 1 model selected  

> select /A:1

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

> select /A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> transparency sel 0

> transparency sel 50

> transparency sel 0

> transparency sel 50

> volume style surface

No volumes specified  

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> volume hide

No volumes specified  

> volume showOutlineBox true

No volumes specified  

> transparency sel 0

> transparency sel 50

> graphics silhouettes true

> set bgColor black

> ui mousemode right "map eraser"

> ui mousemode right "contour level"

Hide dust shortcut requires a displayed map surface  

Can only have one displayed volume when erasing  

[Repeated 1 time(s)]

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 8396 atom styles  

> style sel ball

Changed 8396 atom styles  

> mlp sel

Map values for surface "AF-O00329-F1-model_v4.pdb_A SES surface": minimum
-29.14, mean -4.734, maximum 24.33  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp sel

Map values for surface "AF-O00329-F1-model_v4.pdb_A SES surface": minimum
-29.14, mean -4.734, maximum 24.33  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

[Repeated 1 time(s)]

> rainbow sel

[Repeated 2 time(s)]

> undo

[Repeated 2 time(s)]

> color sel bynucleotide

[Repeated 1 time(s)]

> show sel surfaces

[Repeated 1 time(s)]

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> volume planes z style image imageMode "full region"

No volumes specified  

> open /Users/lulahlyons/Downloads/AF-O00329-F1-model_v4.pdb format pdb

AF-O00329-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate
3-kinase catalytic subunit \u03b4 isoform (O00329) [more info...]  

Chain information for AF-O00329-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit \u03b4 isoform
| PK3CD_HUMAN 1-1044  


Can only have one displayed volume when erasing  

[Repeated 1 time(s)]

> show sel surfaces

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> show sel surfaces

> show sel cartoons

> hide sel cartoons

> hide sel surfaces

> volume showOutlineBox true

No volumes specified  

> volume hide

No volumes specified  

> volume hide

No volumes specified  

> hide sel cartoons

[Repeated 1 time(s)]

> hide sel surfaces

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows false

> lighting shadows true

Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.  

Hide dust shortcut requires a displayed map surface  

> volume style surface

No volumes specified  

> volume style surface

No volumes specified  

> transparency sel 0

> volume style image

No volumes specified  

> select #1/A:825-869

343 atoms, 346 bonds, 45 residues, 1 model selected  

> select #1/A:869-875

61 atoms, 61 bonds, 7 residues, 1 model selected  

> style sel stick

Changed 61 atom styles  

> style sel stick

Changed 61 atom styles  

> undo

[Repeated 1 time(s)]

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select #1/A:1043-1044

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> style sel stick

Changed 8396 atom styles  

> style sel sphere

Changed 8396 atom styles  

> style sel stick

Changed 8396 atom styles  

> style sel ball

Changed 8396 atom styles  

> style sel stick

Changed 8396 atom styles  

> style sel sphere

Changed 8396 atom styles  

> style sel stick

Changed 8396 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> select #1/A:1007-1044

329 atoms, 336 bonds, 38 residues, 1 model selected  

> select #1/A:959-1044

714 atoms, 729 bonds, 86 residues, 1 model selected  

> select #1/A:1044

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

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> hide sel atoms

> select #1/A:830

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

> select #1/A:830-831

17 atoms, 16 bonds, 2 residues, 1 model selected  

> rainbow sel

[Repeated 1 time(s)]

> select #1/A:999-1044

386 atoms, 393 bonds, 46 residues, 1 model selected  

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> rainbow sel

[Repeated 1 time(s)]

> color sel bynucleotide

> rainbow sel

[Repeated 4 time(s)]

> coulombic sel

Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select #1/A:775-776

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #1/A:775-778

31 atoms, 31 bonds, 4 residues, 1 model selected  

> select #1/A:1044

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

> select #1/A:996-1044

415 atoms, 423 bonds, 49 residues, 1 model selected  

> color /A: 830,1044 yellow

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select #1/A:830

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

> select #1/A:830-1044

1746 atoms, 1783 bonds, 215 residues, 1 model selected  

> color sel bychain

[Repeated 1 time(s)]

> color /A: 830,1044 yellow

> color yellow

> undo

> color 830-1044 yellow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A:830-1044 yellow

> color /A:675-830 red

> color /A:500- 675 green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A: 500- 675 green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A: 500-675 green

> color /A: 325-475 teal

> color /A: 189-324 peachpuff

> color /A: 189-324 light pink

> color /A: 1-105 baby blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A: 1-105 light blue

> highlight Val774

highlight is provided by the uninstalled bundle SEQCROW versions 1.8.4 \u2013 1.8.7  

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> Val774

Unknown command: Val774  

> select #1/A:830-1044

1746 atoms, 1783 bonds, 215 residues, 1 model selected  

> select #1/A:1001

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

> select #1/A:1001

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

> select
> #1/A:19-25,31-37,68-73,79-82,98-103,189-196,202-208,239-243,273-278,324-331,340-348,373-376,389-399,413-424,435-440,470-475,759-765,772-780,815-819,822-826,831-833,899-902,907-909

1182 atoms, 1185 bonds, 148 residues, 1 model selected  

> coulombic sel

Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface "AF-O00329-F1-model_v4.pdb_A SES surface": minimum
-29.14, mean -4.734, maximum 24.33  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> coulombic sel

Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select #1/A:828

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

> select #1/A:828

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

> coulombic sel

Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> ui mousemode right "mark point"

> ui mousemode right "mark plane"

> Val828

Unknown command: Val828  

> ui mousemode right translate

> ui mousemode right label

[Repeated 3 time(s)]

> hide sel surfaces

> ui mousemode right label

[Repeated 1 time(s)]

> ui mousemode right distance

> ui mousemode right label

> ui mousemode right "move label"

> ui mousemode right "color key"

> ui mousemode right "move label"

> ui mousemode right "color key"

> key delete

> ui mousemode right "move label"

> save /Users/lulahlyons/Desktop/image2.png supersample 3

> save /Users/lulahlyons/Desktop/image3.png supersample 3

> color sel byhetero

> show sel atoms

> hide sel atoms

> show sel atoms

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select #1/A:661

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:661-707

367 atoms, 372 bonds, 47 residues, 1 model selected  

> select #1/A:676

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

> select #1/A:676-1044

2953 atoms, 3011 bonds, 369 residues, 1 model selected  

> color sel byhetero

> style sel stick

Changed 2953 atom styles  

> color sel bychain

[Repeated 1 time(s)]

> show sel atoms

> color sel bypolymer

> show sel surfaces

> coulombic sel

Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface "AF-O00329-F1-model_v4.pdb_A SES surface": minimum
-29.14, mean -4.734, maximum 24.33  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Coulombic values for AF-O00329-F1-model_v4.pdb_A SES surface #1.1: minimum,
-20.17, mean -1.58, maximum 14.29  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color sel bychain

[Repeated 1 time(s)]

> color sel byhetero

[Repeated 1 time(s)]

> hide sel surfaces

> select #1/A:453-454

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/A:453-457

34 atoms, 34 bonds, 5 residues, 1 model selected  

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #1/A:999-1044

386 atoms, 393 bonds, 46 residues, 1 model selected  

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> select #1/A:1041-1044

37 atoms, 36 bonds, 4 residues, 1 model selected  

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> hide sel atoms

> set bgColor white

> lighting full

[Repeated 1 time(s)]

> lighting shadows false

> lighting flat

> lighting full

> lighting flat

[Repeated 2 time(s)]

> lighting full

[Repeated 9 time(s)]

> lighting soft

[Repeated 4 time(s)]

> lighting simple

[Repeated 3 time(s)]

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

[Repeated 1 time(s)]

> lighting flat

[Repeated 3 time(s)]

> undo

[Repeated 9 time(s)]

> redo

> hide sel atoms

[Repeated 2 time(s)]

> hide sel cartoons

> select #1/A:1044

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

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> hide sel cartoons

[Repeated 1 time(s)]

> hide sel atoms

> show sel surfaces

> hide sel surfaces

> lighting simple

> lighting soft

> lighting full

[Repeated 2 time(s)]

> lighting soft

[Repeated 8 time(s)]

> lighting simple

[Repeated 1 time(s)]

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting full

[Repeated 1 time(s)]

> lighting flat

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting flat

> lighting soft

> lighting flat

> lighting full

> save /Users/lulahlyons/Desktop/image4.png supersample 3

> save /Users/lulahlyons/Desktop/image5.png supersample 3

> save /Users/lulahlyons/Desktop/image6.png supersample 3

> name N-lobe /a:675-830

[Repeated 2 time(s)]

> ui tool show "Selection Inspector"

> select /a:675-830

2448 atoms, 2488 bonds, 312 residues, 2 models selected  

> name frozen N-lobe sel

> ui tool show "Color Key"

> ui mousemode right "color key"

> key delete

> ui mousemode right "move label"

> ui tool show "Marker Placement"

> ui mousemode right "mark point"

> ui mousemode right "mark plane"

> label N-lobe

> ui windowfill toggle

[Repeated 1 time(s)]

> name C-Lobe /a: 830-1044

> label C-lobe

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> name C-lobe /a:830-1044

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

Error executing selector 'C-lobe':  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  

See log for complete Python traceback.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

During handling of the above exception, another exception occurred:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2864, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2640, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2499, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 901, in parse  
return anno.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C-lobe  

grako.exceptions.FailedSemantics: error evaluating selector C-lobe  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  

See log for complete Python traceback.  


> name C-lobe /a:831-1044

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

Error executing selector 'C-lobe':  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  

See log for complete Python traceback.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

During handling of the above exception, another exception occurred:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2864, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2640, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2499, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 901, in parse  
return anno.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C-lobe  

grako.exceptions.FailedSemantics: error evaluating selector C-lobe  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  

See log for complete Python traceback.  


> select 830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:830-1044

Expected an objects specifier or a keyword  

> select /a:831-1044

Expected an objects specifier or a keyword  

> select /a:831-1044

Expected an objects specifier or a keyword  

> select #1/A:777

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

> select #1/A:777-779

28 atoms, 28 bonds, 3 residues, 1 model selected  

> select /a:831-1044

Expected an objects specifier or a keyword  

> select /a:831-1044

Expected an objects specifier or a keyword  

> select /a:831-1044

Expected an objects specifier or a keyword  

> select /A:831-1044

Expected an objects specifier or a keyword  

> select /a:831-1044

Expected an objects specifier or a keyword  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

Error executing selector 'C-Lobe':  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  

See log for complete Python traceback.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

During handling of the above exception, another exception occurred:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1610, in <lambda>  
selectors_menu.triggered.connect(lambda name:
self.select_by_mode(name.text()))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1648, in select_by_mode  
run(self.session, "%s %s" % (cmd, selector_text))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2864, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2640, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2499, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C-Lobe  

grako.exceptions.FailedSemantics: error evaluating selector C-Lobe  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  

See log for complete Python traceback.  


> select /a:831-1044

Expected an objects specifier or a keyword  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

Error executing selector 'C-Lobe':  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  

See log for complete Python traceback.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

During handling of the above exception, another exception occurred:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1610, in <lambda>  
selectors_menu.triggered.connect(lambda name:
self.select_by_mode(name.text()))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1648, in select_by_mode  
run(self.session, "%s %s" % (cmd, selector_text))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2864, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2640, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2499, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector C-Lobe  

grako.exceptions.FailedSemantics: error evaluating selector C-Lobe  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  

See log for complete Python traceback.  


> label /a:831-1044

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label residues /a:831-1044

Expected a keyword  

> label /a:831-1044 residues

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> name c-lobe /a:831-1044

"/a:831-1044 ": contains extra trailing text  

> name c-lobe /a:831-1044

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

Error executing selector 'c-lobe':  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  

See log for complete Python traceback.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

During handling of the above exception, another exception occurred:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2864, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2640, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2499, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 901, in parse  
return anno.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector c-lobe  

grako.exceptions.FailedSemantics: error evaluating selector c-lobe  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  

See log for complete Python traceback.  


> name frozen C-lobe sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

Error executing selector 'c-lobe':  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  

See log for complete Python traceback.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

During handling of the above exception, another exception occurred:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2864, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2640, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2499, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 901, in parse  
return anno.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector c-lobe  

grako.exceptions.FailedSemantics: error evaluating selector c-lobe  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  

See log for complete Python traceback.  


> label /a831-1040

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label /a:831-1040

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label /a:831-1044

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label /a:831-1044 residues

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label /a:831-1044 residues text

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label /a:831-1044 residues text

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> select /a:831-1044 residues text

Expected an objects specifier or a keyword  

> select #1/A:1044

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

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> select /a:831-1044

Expected an objects specifier or a keyword  

> select /a:831-1044

Expected an objects specifier or a keyword  

> select /a:831-1044

Expected an objects specifier or a keyword  

> show sel surfaces

[Repeated 1 time(s)]

> hide sel surfaces

> select /a:831-1044

Expected an objects specifier or a keyword  

> select /a:787

Expected an objects specifier or a keyword  

> select /a: 787

Expected an objects specifier or a keyword  

> select 787

Expected an objects specifier or a keyword  

> select 787

Expected an objects specifier or a keyword  

> select #1/A:959

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

> select #1/A:959-961

27 atoms, 27 bonds, 3 residues, 1 model selected  

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select /A asp787

Expected an objects specifier or a keyword  

> select /A ASP 787

Expected an objects specifier or a keyword  

> select /A Asp787

Expected an objects specifier or a keyword  

> select
> #1/A:19-25,31-37,68-73,79-82,98-103,189-196,202-208,239-243,273-278,324-331,340-348,373-376,389-399,413-424,435-440,470-475,759-765,772-780,815-819,822-826,831-833,899-902,907-909

1182 atoms, 1185 bonds, 148 residues, 1 model selected  

> select #1/A:782

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

> select #1/A:782-783

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select
> #1/A:9-11,42-55,59-61,65-67,89-92,108-121,125-127,129-131,134-156,159-166,213-228,236-238,256-258,260-268,279-289,316-318,381-383,488-497,505-516,525-533,535-541,543-552,558-570,576-583,590-600,605-611,613-620,628-639,641-654,661-674,678-704,708-719,722-728,746-748,785-803,834-841,845-850,854-862,865-888,936-942,950-969,971-984,992-1001,1008-1024,1026-1041

3783 atoms, 3816 bonds, 460 residues, 1 model selected  

> select #1/A:787

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

> select #1/A:787

8 atoms, 7 bonds, 1 residue, 1 model selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

Error executing selector 'c-lobe':  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  

See log for complete Python traceback.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 941, in find_matches  
f(session, models, results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/basic_actions/cmd.py", line 31, in selector  
objects, used, unused = ObjectsArg.parse(spec, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 617, in find_matches  
_add_model_parts(session, model, self.sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 586, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 917, in atomspec_filter  
return self._atomspec_filter_chain(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 933, in _atomspec_filter_chain  
s = numpy.vectorize(choose)(chain_ids)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2372, in __call__  
return self._call_as_normal(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2365, in _call_as_normal  
return self._vectorize_call(func=func, args=vargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2450, in _vectorize_call  
ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/lib/function_base.py", line 2406, in _get_ufunc_and_otypes  
raise ValueError('cannot call `vectorize` on size 0 inputs '  
ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set  

During handling of the above exception, another exception occurred:  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2864, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2640, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2499, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 901, in parse  
return anno.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1309, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1091, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1001, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1004, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  
grako.exceptions.FailedSemantics: error evaluating selector c-lobe  

grako.exceptions.FailedSemantics: error evaluating selector c-lobe  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 945, in find_matches  
raise FailedSemantics("error evaluating selector %s" % self.name)  

See log for complete Python traceback.  


> label /A: 831-1044

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label /A:831-1044

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label residues /A:831-1044

Expected a keyword  

> label residues /A:831-1044

Expected a keyword  

> label residues /A:831-1044

Expected a keyword  

> label #0:831-1044

[Repeated 3 time(s)]

> select #1/A:1044

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

> select #1/A:136-1044

7305 atoms, 7474 bonds, 909 residues, 1 model selected  

> select #1/A:1041-1044

37 atoms, 36 bonds, 4 residues, 1 model selected  

> select #1/A

8396 atoms, 8592 bonds, 1044 residues, 1 model selected  

> label #0:831-1044

[Repeated 4 time(s)]

> select #0:831-1044

Nothing selected  

> select #0:831-1044

Nothing selected  

> select #0:831-1044

Nothing selected  

> select :831-1044

3470 atoms, 3544 bonds, 428 residues, 2 models selected  

> alias define C-lobe sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/alias.py", line 46, in alias  
cli.create_alias(name, text, user=True, logger=logger)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3528, in create_alias  
register(name, alias.cmd_desc(synopsis='alias of "%s"' % text, url=url),  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2349, in register  
_parent_info.add_subcommand(words[-1], name, cmd_desc, logger=logger)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2263, in add_subcommand  
logger.info("FYI: alias is hiding existing command" %  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: not all arguments converted during string formatting  

TypeError: not all arguments converted during string formatting  

File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2263, in add_subcommand  
logger.info("FYI: alias is hiding existing command" %  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  





OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Air
     Model Identifier: Mac14,15
     Model Number: MQKP3B/A
     Chip: Apple M2
     Total Number of Cores: 8 (4 performance and 4 efficiency)
     Memory: 8 GB
     System Firmware Version: 8422.100.650
     OS Loader Version: 8422.100.650

Software:

   System Software Overview:

     System Version: macOS 13.3 (22E8252)
     Kernel Version: Darwin 22.4.0
     Time since boot: 42 days, 7 hours, 43 minutes

Graphics/Displays:

   Apple M2:

     Chipset Model: Apple M2
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 10
     Vendor: Apple (0x106b)
     Metal Support: Metal 3
     Displays:
       Color LCD:
         Display Type: Built-in Liquid Retina Display
         Resolution: 2880 x 1864 Retina
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: Yes
         Connection Type: Internal


Installed Packages:
   alabaster: 0.7.16
   appdirs: 1.4.4
   appnope: 0.1.3
   asttokens: 2.4.1
   Babel: 2.14.0
   backcall: 0.2.0
   beautifulsoup4: 4.11.2
   blockdiag: 3.0.0
   blosc2: 2.0.0
   build: 0.10.0
   certifi: 2022.12.7
   cftime: 1.6.3
   charset-normalizer: 3.3.2
   ChimeraX-AddCharge: 1.5.13
   ChimeraX-AddH: 2.2.5
   ChimeraX-AlignmentAlgorithms: 2.0.1
   ChimeraX-AlignmentHdrs: 3.4.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.12.2
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.1.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.49.1
   ChimeraX-AtomicLibrary: 12.1.5
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.3.2
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.1.2
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.10.5
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2.2
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.3.2
   ChimeraX-ChangeChains: 1.1
   ChimeraX-CheckWaters: 1.3.2
   ChimeraX-ChemGroup: 2.0.1
   ChimeraX-Clashes: 2.2.4
   ChimeraX-ColorActions: 1.0.3
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.5
   ChimeraX-CommandLine: 1.2.5
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.7.1
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.2
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2
   ChimeraX-DistMonitor: 1.4
   ChimeraX-DockPrep: 1.1.3
   ChimeraX-Dssp: 2.0
   ChimeraX-EMDB-SFF: 1.0
   ChimeraX-ESMFold: 1.0
   ChimeraX-FileHistory: 1.0.1
   ChimeraX-FunctionKey: 1.0.1
   ChimeraX-Geometry: 1.3
   ChimeraX-gltf: 1.0
   ChimeraX-Graphics: 1.1.1
   ChimeraX-Hbonds: 2.4
   ChimeraX-Help: 1.2.2
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-Label: 1.1.8
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.1.6
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.1.4
   ChimeraX-MapData: 2.0
   ChimeraX-MapEraser: 1.0.1
   ChimeraX-MapFilter: 2.0.1
   ChimeraX-MapFit: 2.0
   ChimeraX-MapSeries: 2.1.1
   ChimeraX-Markers: 1.0.1
   ChimeraX-Mask: 1.0.2
   ChimeraX-MatchMaker: 2.1.2
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.6.1
   ChimeraX-MedicalToolbar: 1.0.2
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.12.1
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.14
   ChimeraX-ModelPanel: 1.4
   ChimeraX-ModelSeries: 1.0.1
   ChimeraX-Mol2: 2.0.3
   ChimeraX-Mole: 1.0
   ChimeraX-Morph: 1.0.2
   ChimeraX-MouseModes: 1.2
   ChimeraX-Movie: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.1
   ChimeraX-NRRD: 1.1
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.13.1
   ChimeraX-PDB: 2.7.3
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.4
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1
   ChimeraX-PubChem: 2.1
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.1
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.2
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 4.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5.1
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0.2
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.11
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.2
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.12.4
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.1.2
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.2.2
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-TaskManager: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.33.3
   ChimeraX-uniprot: 2.3
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.3.2
   ChimeraX-VIPERdb: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0.1
   ChimeraX-vrml: 1.0
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0.2
   ChimeraX-WebServices: 1.1.3
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.1
   contourpy: 1.2.0
   cxservices: 1.2.2
   cycler: 0.12.1
   Cython: 0.29.33
   debugpy: 1.8.0
   decorator: 5.1.1
   docutils: 0.19
   executing: 2.0.1
   filelock: 3.9.0
   fonttools: 4.47.2
   funcparserlib: 2.0.0a0
   glfw: 2.6.4
   grako: 3.16.5
   h5py: 3.10.0
   html2text: 2020.1.16
   idna: 3.6
   ihm: 0.38
   imagecodecs: 2023.9.18
   imagesize: 1.4.1
   ipykernel: 6.23.2
   ipython: 8.14.0
   ipython-genutils: 0.2.0
   ipywidgets: 8.1.1
   jedi: 0.18.2
   Jinja2: 3.1.2
   jupyter-client: 8.2.0
   jupyter-core: 5.7.1
   jupyterlab-widgets: 3.0.9
   kiwisolver: 1.4.5
   line-profiler: 4.0.2
   lxml: 4.9.2
   lz4: 4.3.2
   MarkupSafe: 2.1.4
   matplotlib: 3.7.2
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   nibabel: 5.0.1
   nptyping: 2.5.0
   numexpr: 2.8.8
   numpy: 1.25.1
   openvr: 1.23.701
   packaging: 21.3
   ParmEd: 3.4.3
   parso: 0.8.3
   pep517: 0.13.0
   pexpect: 4.9.0
   pickleshare: 0.7.5
   pillow: 10.2.0
   pip: 23.0
   pkginfo: 1.9.6
   platformdirs: 4.1.0
   prompt-toolkit: 3.0.43
   psutil: 5.9.5
   ptyprocess: 0.7.0
   pure-eval: 0.2.2
   py-cpuinfo: 9.0.0
   pycollada: 0.7.2
   pydicom: 2.3.0
   Pygments: 2.16.1
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.2801
   pyparsing: 3.0.9
   pyproject-hooks: 1.0.0
   PyQt6-commercial: 6.3.1
   PyQt6-Qt6: 6.3.2
   PyQt6-sip: 13.4.0
   PyQt6-WebEngine-commercial: 6.3.1
   PyQt6-WebEngine-Qt6: 6.3.2
   python-dateutil: 2.8.2
   pytz: 2023.3.post1
   pyzmq: 25.1.2
   qtconsole: 5.4.3
   QtPy: 2.4.1
   RandomWords: 0.4.0
   requests: 2.31.0
   scipy: 1.11.1
   setuptools: 67.4.0
   setuptools-scm: 7.0.5
   sfftk-rw: 0.7.3
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.5
   sphinx: 6.1.3
   sphinx-autodoc-typehints: 1.22
   sphinxcontrib-applehelp: 1.0.8
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.6
   sphinxcontrib-htmlhelp: 2.0.5
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.7
   sphinxcontrib-serializinghtml: 1.1.10
   stack-data: 0.6.3
   superqt: 0.5.0
   tables: 3.8.0
   tcia-utils: 1.5.1
   tifffile: 2023.7.18
   tinyarray: 1.2.4
   tomli: 2.0.1
   tornado: 6.4
   traitlets: 5.9.0
   typing-extensions: 4.9.0
   tzdata: 2023.4
   urllib3: 2.1.0
   wcwidth: 0.2.13
   webcolors: 1.12
   wheel: 0.38.4
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.9

[Eric Pettersen]

Tried a few things but couldn't reproduce the selector problem. I have fixed the last error in the report, due to a missing %s in a format string.