id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4204 Bad sequence-header save disha-gajanan.hiregange@… Eric Pettersen "{{{ 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 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 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 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 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 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 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' -> -> : 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 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 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 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 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 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 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 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 *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' -> -> : 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 }}} " defect feedback normal Sessions Greg Couch all ChimeraX