Bad sequence-header save

[disha-gajanan.hiregange@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
ValueError: error processing: 'tools' -> -> : cannot create weak reference to 'list' object

File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\session.py", line 261, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))

See log for complete Python traceback.

This error was obtained after the side view clipping and was not able to save the session

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\AYGroupUser\Desktop\DBA\IJMS Paper\4ug0.cif" format mmcif

4ug0.cif title:  
Structure of the human 80S ribosome [more info...]  
  
Chain information for 4ug0.cif #1  
---  
Chain | Description  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7A  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13A  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18A  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23A  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27A  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35A  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36A  
Lp | 60S ribosomal protein L37A  
Lr | 60S ribosomal protein L28  
Lz | 60S ribosomal protein L10A  
S2 | 18S ribosomal RNA  
S6 | human initiator met-TRNA-I  
SA | 40S ribosomal protein sa  
SB | 40S ribosomal protein S3A  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17-like  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15A  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | ubiquitin-40S ribosomal protein S27A  
Sg | guanine nucleotide-binding protein subunit β-2-like 1  
  
Non-standard residues in 4ug0.cif #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> set bgColor white

> select #1

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> color sel goldenrod

> select #1/ST

1112 atoms, 1131 bonds, 143 residues, 1 model selected  

> color sel green

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/49G_T_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  

> 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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 619.2  
RMSD between 123 pruned atom pairs is 1.070 angstroms; (across all 143 pairs:
1.848)  
  

> select clear

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #1/ST

Alignment identifier is 1/ST  

> sequence chain #2/S

Alignment identifier is 2/S  

> close

> open "C:\Users\AYGroupUser\Desktop\DBA\IJMS Paper\4ug0.cif" format mmcif

4ug0.cif title:  
Structure of the human 80S ribosome [more info...]  
  
Chain information for 4ug0.cif #1  
---  
Chain | Description  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7A  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13A  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18A  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23A  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27A  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35A  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36A  
Lp | 60S ribosomal protein L37A  
Lr | 60S ribosomal protein L28  
Lz | 60S ribosomal protein L10A  
S2 | 18S ribosomal RNA  
S6 | human initiator met-TRNA-I  
SA | 40S ribosomal protein sa  
SB | 40S ribosomal protein S3A  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17-like  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15A  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | ubiquitin-40S ribosomal protein S27A  
Sg | guanine nucleotide-binding protein subunit β-2-like 1  
  
Non-standard residues in 4ug0.cif #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> select clear

> select #1

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> show sel cartoons

> hide sel atoms

> color sel goldenrod

> select #1/ST

1112 atoms, 1131 bonds, 143 residues, 1 model selected  

> color sel green

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/49G_T_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  

> 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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 619.2  
RMSD between 123 pruned atom pairs is 1.070 angstroms; (across all 143 pairs:
1.848)  
  

> showAlignment true

Unknown command: showAlignment true  

> select clear

> select #1/ST:17

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

> style sel ball

Changed 5 atom styles  

> style sel stick

Changed 5 atom styles  

> select clear

> select #2/S:17

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

> style sel stick

Changed 7 atom styles  

> style sel ball

Changed 7 atom styles  

> show sel atoms

> select #1/ST:17

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

> show sel atoms

> select clear

> select #1/S2

36966 atoms, 41243 bonds, 1121 pseudobonds, 1808 residues, 4 models selected  

> select ~sel

182935 atoms, 194767 bonds, 3116 pseudobonds, 16125 residues, 5 models
selected  

> hide sel cartoons

> select #2/S

1125 atoms, 1146 bonds, 144 residues, 1 model selected  

> show sel cartoons

> select #1/SK

827 atoms, 851 bonds, 98 residues, 1 model selected  

> select #1/ST

1112 atoms, 1131 bonds, 143 residues, 1 model selected  

> show sel cartoons

> select clear

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 619.2  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 123 pruned atom pairs is 1.070 angstroms; (across all 143 pairs:
1.848)  
  

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 619.2  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 123 pruned atom pairs is 1.070 angstroms; (across all 143 pairs:
1.848)  
  

> select clear

> select #2/S:17

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

> color sel red

> select clear

Drag select of 101 residues  

> select clear

> lighting simple

> select #1/ST

1112 atoms, 1131 bonds, 143 residues, 1 model selected  

> color sel lime

> color sel magenta

> color sel forest green

> select clear

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting simple

> lighting simple

> lighting simple

> lighting soft

> lighting soft

> lighting soft

> lighting soft

> lighting soft

> lighting soft

> lighting full

> lighting full

> lighting full

> lighting full

> lighting flat

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> lighting flat

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting simple

> undo

> select clear

> lighting simple

> lighting simple

> lighting soft

> lighting soft

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> lighting full

> lighting simple

> nucleotides atoms

> style nucleic stick

Changed 124560 atom styles  

> nucleotides fill

> style nucleic stick

Changed 124560 atom styles  

> nucleotides tube/slab shape box

> nucleotides atoms

> style nucleic stick

Changed 124560 atom styles  

> color byhetero

> color bychain

> color byhetero

> undo

> undo

> select #2/S:17

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

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

> undo

> undo

> select #2/S:17

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

> ~label sel residues

> select clear

> save C:\Users\AYGroupUser\Desktop\image1.png supersample 3

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/49G_T_MM/model/49_g_t_mm_Ala/pro17.cxs"

[Errno 20] Not a directory: 'C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model
predications/model predications/49G_T_MM/model/49_g_t_mm_Ala'  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/49G_T_MM/49_g_t_ala/pro17.cxs"

[Errno 20] Not a directory: 'C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model
predications/model predications/49G_T_MM/49_g_t_ala'  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/49G_T_MM/model/49_g_t_ala_pro_17.cxs"

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/49G_T_MM/model/49_g_t_ala_pro_17.png" width 727 height 340
> supersample 3

> close #2

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/58_G_C_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  
Associated model.pdb chain S to 4ug0.cif, chain ST with 1 mismatch  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  
Associated model.pdb chain S to 4ug0.cif, chain ST with 1 mismatch  
Chains used in RMSD evaluation for alignment 2: 4ug0.cif #1/ST, model.pdb #2/S  

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 619.2  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 123 pruned atom pairs is 1.067 angstroms; (across all 143 pairs:
1.845)  
  

> show sel atoms

> style sel ball

Changed 5 atom styles  

> style sel ball

Changed 7 atom styles  

> show sel atoms

> color sel red

> select clear

> undo

> select clear

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/58_G_C_MM/model/01/58_g_c_als/pro_20.png" width 790 height 340
> supersample 3

Directory "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model
predications/model predications/58_G_C_MM/model/01/58_g_c_als" does not exist  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/58_G_C_MM/model/58_g_c_ala/pro_20.png" width 790 height 340
> supersample 3

Directory "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model
predications/model predications/58_G_C_MM/model/58_g_c_ala" does not exist  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/58_G_C_MM/model/58_g_c_ala/pro_20.cxs"

[Errno 20] Not a directory: 'C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model
predications/model predications/58_G_C_MM/model/58_g_c_ala'  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/58_G_C_MM/model/58_g_c_ala_pro_20.png" width 790 height 340
> supersample 3

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/58_G_C_MM/model/58_g_c_ala_pro_20.cxs"

> close #2

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/156_G_C_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  
Associated model.pdb chain S to 4ug0.cif, chain ST with 1 mismatch  
Chains used in RMSD evaluation for alignment 3: 4ug0.cif #1/ST, model.pdb #2/S  

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 613.6  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 123 pruned atom pairs is 1.069 angstroms; (across all 143 pairs:
1.848)  
  

> style sel ball

Changed 14 atom styles  

> show sel atoms

> show sel atoms

> style sel ball

Changed 6 atom styles  

> show sel atoms

> color sel red

> select clear

> select clear

> select clear

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/156_G_C_MM/model/01/156_g_c_w_c_52.cxs"

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/156_G_C_MM/model/01/156_g_c_w_c_52.png" width 411 height 340
> supersample 3

> close #2

> select #1/ST

1112 atoms, 1131 bonds, 143 residues, 1 model selected  

> hide sel atoms

> select clear

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/176_C_T_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 618.5  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 123 pruned atom pairs is 1.068 angstroms; (across all 143 pairs:
1.848)  
  

> show sel atoms

> style sel ball

Changed 6 atom styles  

> style sel ball

Changed 11 atom styles  

> show sel atoms

> color sel red

> select clear

> select #1/S2:1540

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/S2:1541

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/S2:1543

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/S2:1542

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> color sel bynucleotide

> color sel bynucleotide

> color sel bynucleotide

> undo

> undo

> undo

> select clear

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/176_C_T_MM/model/01/176_c_t_s_f_59.png" width 806 height 340
> supersample 3

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/176_C_T_MM/model/01/176_c_t_s_f_59.cxs"

> close #2

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/184_C_T_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  
Associated model.pdb chain S to 4ug0.cif, chain ST with 1 mismatch  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  

> select up

Nothing selected  

> undo

> select

219902 atoms, 236012 bonds, 4237 pseudobonds, 17933 residues, 5 models
selected  

> show sel atoms

> show sel atoms

> hide sel atoms

> select clear

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 617.1  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 123 pruned atom pairs is 1.069 angstroms; (across all 143 pairs:
1.848)  
  

> show sel atoms

> style sel ball

Changed 11 atom styles  

> show sel atoms

> color sel red

> select clear

> select #1/S2:1543

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/S2:1543

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1/S2:1542

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/S2:1541

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/S2:1540

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/184_C_T_MM/model/01/184_c_t_r_w_62.cxs"

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/184_C_T_MM/model/01/184_c_t_r_w_62.png" width 737 height 340
> supersample 3

> close #2

> select /ST:62

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

> hide sel atoms

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/185_G_A_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 628.9  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 123 pruned atom pairs is 1.070 angstroms; (across all 143 pairs:
1.848)  
  

> show sel atoms

> show sel atoms

> color sel red

> select clear

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/185_G_A_MM/model/01/185_g_a_r_Q_62.png" width 813 height 340
> supersample 3

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/185_G_A_MM/model/01/185_g_a_r_Q_62.cxs"

> close #2

> open "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/01/model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
S | No description available  
  
Associated model.pdb chain S to 4ug0.cif, chain ST with 1 mismatch  
Chains used in RMSD evaluation for alignment 1: 4ug0.cif #1/ST, model.pdb #2/S  

> mmaker #2 to #1 showAlignment true

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 4ug0.cif, chain ST (#1) with model.pdb, chain S (#2), sequence
alignment score = 617.1  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 4ug0.cif #1/ST, model.pdb #2/S  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 123 pruned atom pairs is 1.068 angstroms; (across all 143 pairs:
1.847)  
  

> style sel ball

Changed 4 atom styles  

> show sel atoms

> show sel atoms

> color sel red

> select #1/S2:1543

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/S2:1542

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/S2:1541

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/S2:1540

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/ST:62@CA

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select #2/S:62

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

> hide sel atoms

> hide sel atoms

> select #1/ST:63

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

> select #1/ST:62@O

1 atom, 1 residue, 1 model selected  

> select #2/S:62

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

> select #1/ST:62@CA

1 atom, 1 residue, 1 model selected  

> select #1/ST:62@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> hide sel atoms

> select clear

> select #1/S2:1576

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/S2:1563

23 atoms, 25 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 23 atom styles  

> style sel ball

Changed 23 atom styles  

> show sel atoms

> select #1/S2:1562

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/S2:1561

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/S2:1564

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> ui tool show "Side View"

> ui tool show "Side View"

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/01/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/01/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.png" width 764 height 323
> supersample 3

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs" includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> ui tool show "Side View"

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model
> predications/212_G_A_MM/model/212_g_a_g_e_71.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, 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 "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 292, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 47, in __init__  
self.alignment = proxy(alignment)  
TypeError: cannot create weak reference to 'list' object  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 826, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000001FE88E39888> -> <chimerax.seq-view.tool.SequenceViewer object at
0x000001FECFBACE88>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 452.41
OpenGL renderer: GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Latitude 5401
OS: Microsoft Windows 10 Enterprise LTSC (Build 17763)
Memory: 34,131,316,736
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9850H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

[Eric Pettersen]

Hi Disha,

It is a mystery to me how this error can occur. The session is trying to save an object it should not be trying to save. If you are willing, it would help me if you sent me these two files:

C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model predications/185_G_A_MM/model/01/185_g_a_r_Q_62.cxs
C:/Users/AYGroupUser/Desktop/DBA/IJMS Paper/model predications/model predications/212_G_A_MM/model/01/model.pdb

...which should allow me to get to the state you were at not long before the error occurred and then I can try executing the same commands shown in the log between when you saved the above session and when the error happened. You could send them to me directly (pett@…) if you don't want them to be in this ticket.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Greg Couch]

When you get the .cxs file, use "debug sdump foo.cxs foo.txt" command to convert the session file to text. You should then be able to track down which object refers to what.

The first error in the traceback is "TypeError: cannot create weak reference to 'list' object". Was the alignment properly saved as a list and not converted back correctly?

[Eric Pettersen]

Replying to Greg Couch:

The first error in the traceback is "TypeError: cannot create weak reference to 'list' object". Was the alignment properly saved as a list and not converted back correctly?

The problem is that alignment header objects inherit from list, and the generic session code is trying to initialize it with a list of its own contents, and that is not what its constructor takes. The constructor expects the first argument to be an alignment, which it tries to make a weak reference to, not a list.