Can't save session because NewerVersionQuery not listed

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.7.dev202309272145 (2023-09-27 21:45:56 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
Registration file '/Users/svearikeoeverdieck/Library/Application
Support/ChimeraX/registration' has expired  
  
UCSF ChimeraX version: 1.7.dev202309272145 (2023-09-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/6dfh_63_134_180_202_265_294/af3/hits/sequence24/sequence24_model.cif

Chain information for sequence24_model.cif #1  
---  
Chain | Description  
A B C | .  
  
Color sequence24_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/6dfh_63_134_180_202_265_294/af3/hits/sequence158/sequence158_model.cif

Chain information for sequence158_model.cif #2  
---  
Chain | Description  
A B C | .  
  
Color sequence158_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/6dfh_63_134_180_202_265_294/af3/hits/sequence143/sequence143_model.cif

Chain information for sequence143_model.cif #3  
---  
Chain | Description  
A B C | .  
  
Color sequence143_model.cif by residue attribute pLDDT_score  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence158_model.cif,
chain A (#2), sequence alignment score = 1255  
RMSD between 153 pruned atom pairs is 1.047 angstroms; (across all 310 pairs:
4.992)  
  

> mmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence143_model.cif,
chain C (#3), sequence alignment score = 1275  
RMSD between 168 pruned atom pairs is 0.956 angstroms; (across all 310 pairs:
5.139)  
  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence211_model.cif

Chain information for sequence211_model.cif #4  
---  
Chain | Description  
A B C | .  
  
Color sequence211_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence93_model.cif

Chain information for sequence93_model.cif #5  
---  
Chain | Description  
A B C | .  
  
Color sequence93_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence62_data.json

sequence62_data.json does not look like Mole Online json file, does not
contain Channels.  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence132_model.cif

Chain information for sequence132_model.cif #6  
---  
Chain | Description  
A B C | .  
  
Color sequence132_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence62_model.cif

Chain information for sequence62_model.cif #7  
---  
Chain | Description  
A B C | .  
  
Color sequence62_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence233_model.cif

Chain information for sequence233_model.cif #8  
---  
Chain | Description  
A B C | .  
  
Color sequence233_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence183_model.cif

Chain information for sequence183_model.cif #9  
---  
Chain | Description  
A B C | .  
  
Color sequence183_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence187_model.cif

Chain information for sequence187_model.cif #10  
---  
Chain | Description  
A B C | .  
  
Color sequence187_model.cif by residue attribute pLDDT_score  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250728_design7_2s_wrec2/20250807_6dfh_63_138_180_202_265_294/af3/hits/sequence7_model.cif

Chain information for sequence7_model.cif #11  
---  
Chain | Description  
A B C | .  
  
Color sequence7_model.cif by residue attribute pLDDT_score  

> mmaker #4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence211_model.cif,
chain A (#4), sequence alignment score = 1155  
RMSD between 163 pruned atom pairs is 1.165 angstroms; (across all 310 pairs:
5.666)  
  

> mmaker #5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence93_model.cif, chain
A (#5), sequence alignment score = 1175.6  
RMSD between 135 pruned atom pairs is 1.139 angstroms; (across all 310 pairs:
5.027)  
  

> mmaker #6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence132_model.cif,
chain A (#6), sequence alignment score = 1110.1  
RMSD between 145 pruned atom pairs is 0.985 angstroms; (across all 310 pairs:
5.278)  
  

> mmaker #7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence62_model.cif, chain
C (#7), sequence alignment score = 1118.1  
RMSD between 82 pruned atom pairs is 0.980 angstroms; (across all 310 pairs:
4.616)  
  

> mmaker #8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence233_model.cif,
chain C (#8), sequence alignment score = 1140.2  
RMSD between 170 pruned atom pairs is 1.198 angstroms; (across all 310 pairs:
5.425)  
  

> mmaker #9 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence183_model.cif,
chain A (#9), sequence alignment score = 1146.2  
RMSD between 147 pruned atom pairs is 1.043 angstroms; (across all 310 pairs:
5.505)  
  

> mmaker #10 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence187_model.cif,
chain A (#10), sequence alignment score = 1147.4  
RMSD between 157 pruned atom pairs is 0.985 angstroms; (across all 310 pairs:
5.959)  
  

> mmaker #11 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence7_model.cif, chain
A (#11), sequence alignment score = 1125.3  
RMSD between 139 pruned atom pairs is 1.092 angstroms; (across all 310 pairs:
6.208)  
  

> open
> /Volumes/soever/scratch/apex_cage/with_helix/base_design7/20250722_reintroduce_moreapexres/6dfh/af3_msa_2/hits/sequence4_model.cif

Chain information for sequence4_model.cif #12  
---  
Chain | Description  
A B C | .  
  
Color sequence4_model.cif by residue attribute pLDDT_score  

> mmaker #12 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence4_model.cif, chain
A (#12), sequence alignment score = 1145.6  
RMSD between 166 pruned atom pairs is 0.991 angstroms; (across all 309 pairs:
5.714)  
  

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #12 models

> mmaker #7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with sequence62_model.cif, chain
C (#7), sequence alignment score = 1118.1  
RMSD between 82 pruned atom pairs is 0.980 angstroms; (across all 310 pairs:
4.616)  
  

> ui tool show Matchmaker

> matchmaker #7/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain A (#1) with sequence62_model.cif, chain
A (#7), sequence alignment score = 1086.9  
RMSD between 83 pruned atom pairs is 0.992 angstroms; (across all 310 pairs:
4.595)  
  

> hide #7 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #4 models

> open
> /Volumes/soever/apex_cage/with_helix/base_design7/pdbs/pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb

Chain information for
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb
#13  
---  
Chain | Description  
A B C | No description available  
  

> mmaker #13 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker sequence24_model.cif, chain C (#1) with
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13), sequence alignment score = 542.1  
RMSD between 148 pruned atom pairs is 1.142 angstroms; (across all 306 pairs:
4.957)  
  

> hide #4 models

> mmaker #2 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence158_model.cif, chain A (#2), sequence alignment
score = 501  
RMSD between 154 pruned atom pairs is 1.076 angstroms; (across all 297 pairs:
4.229)  
  

> mmaker #3 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence143_model.cif, chain C (#3), sequence alignment
score = 535.9  
RMSD between 164 pruned atom pairs is 1.015 angstroms; (across all 309 pairs:
4.147)  
  

> mmaker #4 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence211_model.cif, chain A (#4), sequence alignment
score = 693.8  
RMSD between 240 pruned atom pairs is 1.080 angstroms; (across all 310 pairs:
1.835)  
  

> mmaker #5 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain C (#13) with sequence93_model.cif, chain A (#5), sequence alignment
score = 659.3  
RMSD between 214 pruned atom pairs is 0.946 angstroms; (across all 308 pairs:
3.232)  
  

> mmaker #6 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence132_model.cif, chain A (#6), sequence alignment
score = 704.2  
RMSD between 243 pruned atom pairs is 1.034 angstroms; (across all 310 pairs:
2.120)  
  

> mmaker #7 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence62_model.cif, chain C (#7), sequence alignment
score = 662.3  
RMSD between 197 pruned atom pairs is 1.026 angstroms; (across all 304 pairs:
3.191)  
  

> mmaker #8 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence233_model.cif, chain C (#8), sequence alignment
score = 691.7  
RMSD between 235 pruned atom pairs is 1.122 angstroms; (across all 310 pairs:
1.941)  
  

> mmaker #9 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence183_model.cif, chain A (#9), sequence alignment
score = 701.6  
RMSD between 214 pruned atom pairs is 1.178 angstroms; (across all 310 pairs:
1.993)  
  

> mmaker #10 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence187_model.cif, chain A (#10), sequence alignment
score = 717.2  
RMSD between 215 pruned atom pairs is 1.067 angstroms; (across all 310 pairs:
2.200)  
  

> mmaker #11 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain C (#13) with sequence7_model.cif, chain A (#11), sequence alignment
score = 669.5  
RMSD between 187 pruned atom pairs is 1.104 angstroms; (across all 305 pairs:
3.529)  
  

> mmaker #12 to #13

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
pdiff_desing7_2s_t20_n0.5_gp1_g2dquadratic_pdiff_desing7_2s_wrec_2_renumbered.pdb,
chain B (#13) with sequence4_model.cif, chain A (#12), sequence alignment
score = 699.9  
RMSD between 231 pruned atom pairs is 1.172 angstroms; (across all 310 pairs:
2.222)  
  

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 models

> show #6 models

> hide #6 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #9 models

> hide #9 models

> show #10 models

> hide #10 models

> show #11 models

> hide #11 models

> show #12 models

> hide #12 models

> show #12 models

> save /Users/svearikeoeverdieck/Desktop/design7_2s_wrec2.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj  
raise RuntimeError(  
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x104cdeb50>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj  
raise RuntimeError(  
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x104cdeb50>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save /Users/svearikeoeverdieck/Desktop/design7_2s_wrec2.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj  
raise RuntimeError(  
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x104cdeb50>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj  
raise RuntimeError(  
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x104cdeb50>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: en_US.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 Pro
      Model Identifier: Mac14,9
      Model Number: Z17G002THN/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 1 hour, 53 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.0
    Babel: 2.12.1
    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: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.11.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.48
    ChimeraX-AtomicLibrary: 10.1
    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: 1.0.3
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.4
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202309272145
    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: 1.1.2
    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: 1.2.1
    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
    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: 1.5.12
    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: 1.11
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    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: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.10
    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: 1.12.2
    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: 1.32.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.4
    contourpy: 1.1.1
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.42.1
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    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: 5.3.2
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.10.0
    prompt-toolkit: 3.0.39
    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: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.0
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.2
    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: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.0.5
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9