Alignment headers somehow being directly saved in sessions

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/real_YFVh_ZIKVh_v1.cxs

Log from Sat Sep 20 10:07:17 2025UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_3//MK333798.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1029.27 353.369 1134.96 7430.51 251.82 -197.311 -76.6789 0 -1654.42
-72.4443 210.118 0 0 -27.823 -65.4589 0 -2.28006e+06 0 0 0 0 0 0 0 0
-2.2738e+06  
  
135 messages similar to the above omitted  
  
Chain information for MK333798.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KX156775.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb  
---  
warnings | Ignored bad PDB record found on line 3858  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3859  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_1//KU744693.pdb  
  
Ignored bad PDB record found on line 3860  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3861  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3862  
pose -1013.85 420.253 1172.72 7447.29 238.564 -157.715 -140.325 0 -3515.49
-114.963 256.24 0 0 -24.0578 -136.248 0 -4.30881e+06 0 0 0 0 0 0 0 0
-4.30438e+06  
  
122 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KX156775.pdb  
---  
warnings | Ignored bad PDB record found on line 2286  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 2287  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set__2//KX156775.pdb  
  
Ignored bad PDB record found on line 2288  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 2289  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 2290  
pose -499.01 188.106 566.733 4047.27 138.152 -101.088 -39.8633 0 -545.871
-4.59121 131.926 0 0 -22.4707 -18.1493 0 -1.30524e+06 0 0 0 0 0 0 0 0
-1.3014e+06  
  
73 messages similar to the above omitted  
  
Chain information for KU744693.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for KX156775.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #3/A

Alignment identifier is 3/A  

> select #1/A:112-133

708 atoms, 764 bonds, 22 residues, 1 model selected  

> select #1/A:119-133

480 atoms, 517 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/A:120

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:106-120

487 atoms, 527 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3/A:71

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #3/A:57-71

487 atoms, 527 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show Matchmaker

> matchmaker #1,3 to #2 showAlignment true

No chains in reference structure KU744693.pdb #2 compatible with BLOSUM-62
similarity matrix  

> ui tool show Matchmaker

> matchmaker #1,3 to #2 matrix Nucleic showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 KU744693.pdb, chain A (#2) with MK333798.pdb, chain A (#1),
sequence alignment score = 157.7  
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: MK333798.pdb #1/A,
KU744693.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 9 pruned atom pairs is 0.638 angstroms; (across all 93 pairs:
52.163)  
  
Matchmaker KU744693.pdb, chain A (#2) with KX156775.pdb, chain A (#3),
sequence alignment score = 250.1  
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: KU744693.pdb #2/A,
KX156775.pdb #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 14 pruned atom pairs is 0.916 angstroms; (across all 55 pairs:
46.283)  
  

> select #2/A:54

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:54-69 #3/A:4-19

1031 atoms, 1113 bonds, 32 residues, 2 models selected  
Seqview [ID: 2] region KU744693.pdb, chain A..KX156775.pdb, chain A [54-69]
RMSD: 1.111  
  

> select #2/A:54

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:54-68 #1/A:59-73

961 atoms, 1036 bonds, 30 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [62-76]
RMSD: 2.392  
  

> select clear

> select #2/A:54-69 #3/A:4-19

1031 atoms, 1113 bonds, 32 residues, 2 models selected  
Seqview [ID: 2] region Cα RMSD..KX156775.pdb, chain A [54-69] RMSD: 1.111  
  

> select clear

> select #2/A:54

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:43-54 #1/A:51-59

683 atoms, 738 bonds, 21 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [51-62]
RMSD: 13.356  
  

> select #1/A:83

31 atoms, 32 bonds, 1 residue, 1 model selected  

> select #1/A:89 #2/A:78

60 atoms, 62 bonds, 2 residues, 2 models selected  

> select clear

> select clear

> select #2/A:57-61,65-68 #1/A:62-66,70-73

577 atoms, 619 bonds, 18 residues, 2 models selected  

> select #2/A:30

31 atoms, 32 bonds, 1 residue, 1 model selected  

> select #2/A:30-33 #1/A:38-41

258 atoms, 277 bonds, 8 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [38-41]
RMSD: 48.489  
  

> select #2/A:57

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:57-68 #1/A:62-73

764 atoms, 822 bonds, 24 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [65-76]
RMSD: 0.680  
  

> select #3/A

1788 atoms, 1928 bonds, 56 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/1YFVh_allZIKVh_superSelected3.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 293, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024721F2BE80>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 293, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024721F2BE80>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/1YFVh_allZIKVh_selected3.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 293, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024721F2BE80>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 293, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024721F2BE80>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/1YFVh_allZIKVh_super3.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 293, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024721F2BE80>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 293, in process  
return copy_state(data, convert=convert)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 215, in copy_state  
return _copy(data)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 200, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in _copy  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 209, in <listcomp>  
items = [_copy(o) for o in data]  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\state.py", line 210, in _copy  
return data.__class__(items)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 29, in __init__  
super().__init__(alignment, *args, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\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 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024721F2BE80>: cannot create weak reference to 'list' object  
  
ValueError: error processing: 'tools' -> -> : cannot create weak reference to
'list' object  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> select #2/A:1-56 #1/A:1-61

3751 atoms, 4046 bonds, 117 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [1-64]
RMSD: 62.231  
  

> select #1/A:82 #2/A:77

60 atoms, 62 bonds, 2 residues, 2 models selected  

> select clear

> select #2/A:57

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:57-68 #1/A:62-73

764 atoms, 822 bonds, 24 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [65-76]
RMSD: 0.680  
  

> select #2/A:1-56 #1/A:1-61

3751 atoms, 4046 bonds, 117 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [1-64]
RMSD: 62.231  
  

> delete atoms sel

> delete bonds sel

> select #2/A:69

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:69-105 #1/A:74-118

2626 atoms, 2833 bonds, 82 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [77-146]
RMSD: 41.315  
  

> select #2/A:69

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:69-105 #1/A:74-118

2626 atoms, 2833 bonds, 82 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [77-146]
RMSD: 41.315  
  

> delete atoms sel

> delete bonds sel

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY1', defaulting
to 96 DPI.  

monitorData: Unable to obtain handle for monitor '\\\\.\DISPLAY4', defaulting
to 96 DPI.  

> select

764 atoms, 822 bonds, 24 residues, 2 models selected  

> select clear

> select #2/A:57

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:57-68 #1/A:62-73

764 atoms, 822 bonds, 24 residues, 2 models selected  
Seqview [ID: 1] region KU744693.pdb, chain A..MK333798.pdb, chain A [65-76]
RMSD: 0.680  
  

> close session

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KX156775.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KY765324.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MN566104.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MT377500.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OL450365.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OQ661915.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb  
---  
warnings | Ignored bad PDB record found on line 3858  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3859  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_1//KU744693.pdb  
  
Ignored bad PDB record found on line 3860  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3861  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3862  
pose -1013.85 420.253 1172.72 7447.29 238.564 -157.715 -140.325 0 -3515.49
-114.963 256.24 0 0 -24.0578 -136.248 0 -4.30881e+06 0 0 0 0 0 0 0 0
-4.30438e+06  
  
122 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KX156775.pdb  
---  
warnings | Ignored bad PDB record found on line 2286  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 2287  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set__2//KX156775.pdb  
  
Ignored bad PDB record found on line 2288  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 2289  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 2290  
pose -499.01 188.106 566.733 4047.27 138.152 -101.088 -39.8633 0 -545.871
-4.59121 131.926 0 0 -22.4707 -18.1493 0 -1.30524e+06 0 0 0 0 0 0 0 0
-1.3014e+06  
  
73 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KY765324.pdb  
---  
warnings | Ignored bad PDB record found on line 3350  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3351  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_2//KY765324.pdb  
  
Ignored bad PDB record found on line 3352  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3353  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3354  
pose -872.229 367.381 993.473 6388.86 205.302 -141.651 -101.052 0 -2381.14
-62.4463 264.55 0 0 -19.6615 -91.4706 0 -2.41393e+06 0 0 0 0 0 0 0 0
-2.40938e+06  
  
106 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MN566104.pdb  
---  
warnings | Ignored bad PDB record found on line 3926  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3927  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_5_2//MN566104.pdb  
  
Ignored bad PDB record found on line 3928  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3929  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3930  
pose -1003.85 401.899 1156.76 7932.68 239.907 -154.907 -135.941 0 -2776.8
-78.0478 284.545 0 0 -34.1555 -116.927 0 -3.7059e+06 0 0 0 0 0 0 0 0
-3.70019e+06  
  
124 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MT377500.pdb  
---  
warnings | Ignored bad PDB record found on line 3926  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3927  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_4//MT377500.pdb  
  
Ignored bad PDB record found on line 3928  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3929  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3930  
pose -1065.51 450.568 1227.31 7661.04 240.846 -164.159 -137.301 0 -3292.41
-88.2398 292.578 0 0 -28.1659 -129.13 0 -3.72918e+06 0 0 0 0 0 0 0 0
-3.72421e+06  
  
124 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OL450365.pdb  
---  
warnings | Ignored bad PDB record found on line 3926  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3927  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_5//OL450365.pdb  
  
Ignored bad PDB record found on line 3928  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3929  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3930  
pose -1036.63 443.868 1195.34 7062.28 232.704 -161.488 -125.192 0 -2857.61
-81.638 215.057 0 0 -36.2418 -119.645 0 -3.71233e+06 0 0 0 0 0 0 0 0
-3.7076e+06  
  
124 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OQ661915.pdb  
---  
warnings | Ignored bad PDB record found on line 3419  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3420  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_5_2//OQ661915.pdb  
  
Ignored bad PDB record found on line 3421  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3422  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3423  
pose -825.377 338.598 953.262 6411.87 205.602 -152.122 -93.4969 0 -1593.46
-34.6623 165.632 0 0 -31.6973 -57.6649 0 -2.12298e+06 0 0 0 0 0 0 0 0
-2.11769e+06  
  
108 messages similar to the above omitted  
  
Chain information for KU744693.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for KX156775.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for KY765324.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for MN566104.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for MT377500.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for OL450365.pdb #6  
---  
Chain | Description  
A | No description available  
  
Chain information for OQ661915.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/OR119828.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_3//MK333798.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1029.27 353.369 1134.96 7430.51 251.82 -197.311 -76.6789 0 -1654.42
-72.4443 210.118 0 0 -27.823 -65.4589 0 -2.28006e+06 0 0 0 0 0 0 0 0
-2.2738e+06  
  
135 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/OR119828.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_3_//OR119828.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1031.29 354.331 1142.81 7453.57 255.115 -191.635 -81.9594 0 -1558.49
-58.7762 234.354 0 0 -27.7766 -68.4859 0 -2.28156e+06 0 0 0 0 0 0 0 0
-2.27514e+06  
  
135 messages similar to the above omitted  
  
Chain information for MK333798.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for OR119828.pdb #9  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-9 to #1 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KU744693.pdb, chain A (#1) with KX156775.pdb, chain A (#2),
sequence alignment score = 259.1  
RMSD between 14 pruned atom pairs is 0.980 angstroms; (across all 70 pairs:
46.415)  
  
Matchmaker KU744693.pdb, chain A (#1) with KY765324.pdb, chain A (#3),
sequence alignment score = 396  
RMSD between 22 pruned atom pairs is 1.148 angstroms; (across all 103 pairs:
35.021)  
  
Matchmaker KU744693.pdb, chain A (#1) with MN566104.pdb, chain A (#4),
sequence alignment score = 429.7  
RMSD between 28 pruned atom pairs is 1.149 angstroms; (across all 120 pairs:
14.867)  
  
Matchmaker KU744693.pdb, chain A (#1) with MT377500.pdb, chain A (#5),
sequence alignment score = 429.7  
RMSD between 20 pruned atom pairs is 1.214 angstroms; (across all 120 pairs:
17.127)  
  
Matchmaker KU744693.pdb, chain A (#1) with OL450365.pdb, chain A (#6),
sequence alignment score = 429.7  
RMSD between 7 pruned atom pairs is 1.297 angstroms; (across all 120 pairs:
24.073)  
  
Matchmaker KU744693.pdb, chain A (#1) with OQ661915.pdb, chain A (#7),
sequence alignment score = 399.1  
RMSD between 25 pruned atom pairs is 1.363 angstroms; (across all 105 pairs:
40.428)  
  
Matchmaker KU744693.pdb, chain A (#1) with MK333798.pdb, chain A (#8),
sequence alignment score = 116.2  
RMSD between 4 pruned atom pairs is 0.975 angstroms; (across all 117 pairs:
48.515)  
  
Matchmaker KU744693.pdb, chain A (#1) with OR119828.pdb, chain A (#9),
sequence alignment score = 116.2  
RMSD between 3 pruned atom pairs is 1.051 angstroms; (across all 117 pairs:
42.971)  
  

> matchmaker #1-7,9 to #8 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker MK333798.pdb, chain A (#8) with KU744693.pdb, chain A (#1),
sequence alignment score = 116.2  
RMSD between 4 pruned atom pairs is 0.975 angstroms; (across all 117 pairs:
48.515)  
  
Matchmaker MK333798.pdb, chain A (#8) with KX156775.pdb, chain A (#2),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 71 pairs:
36.101)  
  
Matchmaker MK333798.pdb, chain A (#8) with KY765324.pdb, chain A (#3),
sequence alignment score = 95.8  
RMSD between 4 pruned atom pairs is 1.071 angstroms; (across all 103 pairs:
34.030)  
  
Matchmaker MK333798.pdb, chain A (#8) with MN566104.pdb, chain A (#4),
sequence alignment score = 114.4  
RMSD between 4 pruned atom pairs is 1.104 angstroms; (across all 111 pairs:
39.436)  
  
Matchmaker MK333798.pdb, chain A (#8) with MT377500.pdb, chain A (#5),
sequence alignment score = 114.4  
RMSD between 4 pruned atom pairs is 1.197 angstroms; (across all 111 pairs:
39.178)  
  
Matchmaker MK333798.pdb, chain A (#8) with OL450365.pdb, chain A (#6),
sequence alignment score = 114.4  
RMSD between 5 pruned atom pairs is 1.082 angstroms; (across all 111 pairs:
33.869)  
  
Matchmaker MK333798.pdb, chain A (#8) with OQ661915.pdb, chain A (#7),
sequence alignment score = 95.3  
RMSD between 5 pruned atom pairs is 0.942 angstroms; (across all 105 pairs:
30.725)  
  
Matchmaker MK333798.pdb, chain A (#8) with OR119828.pdb, chain A (#9),
sequence alignment score = 532  
RMSD between 103 pruned atom pairs is 0.715 angstroms; (across all 133 pairs:
5.170)  
  

> close session

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/OR119828.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_3//MK333798.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1029.27 353.369 1134.96 7430.51 251.82 -197.311 -76.6789 0 -1654.42
-72.4443 210.118 0 0 -27.823 -65.4589 0 -2.28006e+06 0 0 0 0 0 0 0 0
-2.2738e+06  
  
135 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/OR119828.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_3_//OR119828.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1031.29 354.331 1142.81 7453.57 255.115 -191.635 -81.9594 0 -1558.49
-58.7762 234.354 0 0 -27.7766 -68.4859 0 -2.28156e+06 0 0 0 0 0 0 0 0
-2.27514e+06  
  
135 messages similar to the above omitted  
  
Chain information for MK333798.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for OR119828.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/KX156775.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/KX156775.pdb  
---  
warnings | Ignored bad PDB record found on line 2286  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 2287  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set__2//KX156775.pdb  
  
Ignored bad PDB record found on line 2288  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 2289  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 2290  
pose -499.01 188.106 566.733 4047.27 138.152 -101.088 -39.8633 0 -545.871
-4.59121 131.926 0 0 -22.4707 -18.1493 0 -1.30524e+06 0 0 0 0 0 0 0 0
-1.3014e+06  
  
73 messages similar to the above omitted  
  
Chain information for KX156775.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-3 to #1 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker MK333798.pdb, chain A (#1) with OR119828.pdb, chain A (#2),
sequence alignment score = 532  
RMSD between 103 pruned atom pairs is 0.715 angstroms; (across all 133 pairs:
5.170)  
  
Matchmaker MK333798.pdb, chain A (#1) with KX156775.pdb, chain A (#3),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 71 pairs:
36.101)  
  

> matchmaker #3 to #2 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker OR119828.pdb, chain A (#2) with KX156775.pdb, chain A (#3),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> matchmaker #1-2 to #3 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KX156775.pdb, chain A (#3) with MK333798.pdb, chain A (#1),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 71 pairs:
36.101)  
  
Matchmaker KX156775.pdb, chain A (#3) with OR119828.pdb, chain A (#2),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> matchmaker #1 to #2 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker OR119828.pdb, chain A (#2) with MK333798.pdb, chain A (#1),
sequence alignment score = 532  
RMSD between 103 pruned atom pairs is 0.715 angstroms; (across all 133 pairs:
5.170)  
  

> matchmaker #1,3 to #2 matrix Nucleic gapExtend 20

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 20  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker OR119828.pdb, chain A (#2) with MK333798.pdb, chain A (#1),
sequence alignment score = 532  
RMSD between 103 pruned atom pairs is 0.715 angstroms; (across all 133 pairs:
5.170)  
  
Matchmaker OR119828.pdb, chain A (#2) with KX156775.pdb, chain A (#3),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> matchmaker #1,3 to #2 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker OR119828.pdb, chain A (#2) with MK333798.pdb, chain A (#1),
sequence alignment score = 532  
RMSD between 103 pruned atom pairs is 0.715 angstroms; (across all 133 pairs:
5.170)  
  
Matchmaker OR119828.pdb, chain A (#2) with KX156775.pdb, chain A (#3),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> matchmaker #3 to #2 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker OR119828.pdb, chain A (#2) with KX156775.pdb, chain A (#3),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> select #1/A

4261 atoms, 4599 bonds, 133 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #3/A

Alignment identifier is 3/A  

> select #2/A:133

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:119-133

480 atoms, 517 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3/A:43-71

935 atoms, 1010 bonds, 29 residues, 1 model selected  

> select #3/A:57-71

487 atoms, 527 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> matchmaker #3 to #2 matrix Nucleic gapExtend 10 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker OR119828.pdb, chain A (#2) with KX156775.pdb, chain A (#3),
sequence alignment score = 60.2  
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: OR119828.pdb #2/A,
KX156775.pdb #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 8 pruned atom pairs is 0.971 angstroms; (across all 56 pairs:
39.387)  
  

> select #2/A:64

31 atoms, 32 bonds, 1 residue, 1 model selected  

> select #2/A:64-72 #3/A:16-24

573 atoms, 616 bonds, 18 residues, 2 models selected  
Seqview [ID: 1] region OR119828.pdb, chain A..KX156775.pdb, chain A [64-72]
RMSD: 0.975  
  

> close session

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_3//MK333798.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1029.27 353.369 1134.96 7430.51 251.82 -197.311 -76.6789 0 -1654.42
-72.4443 210.118 0 0 -27.823 -65.4589 0 -2.28006e+06 0 0 0 0 0 0 0 0
-2.2738e+06  
  
135 messages similar to the above omitted  
  
Chain information for MK333798.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb  
---  
warnings | Ignored bad PDB record found on line 3858  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3859  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_1//KU744693.pdb  
  
Ignored bad PDB record found on line 3860  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3861  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3862  
pose -1013.85 420.253 1172.72 7447.29 238.564 -157.715 -140.325 0 -3515.49
-114.963 256.24 0 0 -24.0578 -136.248 0 -4.30881e+06 0 0 0 0 0 0 0 0
-4.30438e+06  
  
122 messages similar to the above omitted  
  
Chain information for KU744693.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2 to #1 matrix Nucleic gapExtend 10 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker MK333798.pdb, chain A (#1) with KU744693.pdb, chain A (#2),
sequence alignment score = 116.2  
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: MK333798.pdb #1/A,
KU744693.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 4 pruned atom pairs is 0.975 angstroms; (across all 117 pairs:
48.515)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> select #1/A:133

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #1/A:119-133

480 atoms, 517 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/A:120

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:106-120

487 atoms, 527 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show Matchmaker

> matchmaker #2 to #1 matrix Nucleic gapExtend 10 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker MK333798.pdb, chain A (#1) with KU744693.pdb, chain A (#2),
sequence alignment score = 98.2  
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: MK333798.pdb #1/A,
KU744693.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 5 pruned atom pairs is 1.546 angstroms; (across all 102 pairs:
54.416)  
  

> matchmaker #1 to #2 matrix Nucleic gapExtend 10 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KU744693.pdb, chain A (#2) with MK333798.pdb, chain A (#1),
sequence alignment score = 98.2  
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: MK333798.pdb #1/A,
KU744693.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 5 pruned atom pairs is 1.546 angstroms; (across all 102 pairs:
54.416)  
  

> close session

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KX156775.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KY765324.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MN566104.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MT377500.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OL450365.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OQ661915.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KU744693.pdb  
---  
warnings | Ignored bad PDB record found on line 3858  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3859  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_1//KU744693.pdb  
  
Ignored bad PDB record found on line 3860  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3861  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3862  
pose -1013.85 420.253 1172.72 7447.29 238.564 -157.715 -140.325 0 -3515.49
-114.963 256.24 0 0 -24.0578 -136.248 0 -4.30881e+06 0 0 0 0 0 0 0 0
-4.30438e+06  
  
122 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KX156775.pdb  
---  
warnings | Ignored bad PDB record found on line 2286  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 2287  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set__2//KX156775.pdb  
  
Ignored bad PDB record found on line 2288  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 2289  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 2290  
pose -499.01 188.106 566.733 4047.27 138.152 -101.088 -39.8633 0 -545.871
-4.59121 131.926 0 0 -22.4707 -18.1493 0 -1.30524e+06 0 0 0 0 0 0 0 0
-1.3014e+06  
  
73 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/KY765324.pdb  
---  
warnings | Ignored bad PDB record found on line 3350  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3351  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_2//KY765324.pdb  
  
Ignored bad PDB record found on line 3352  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3353  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3354  
pose -872.229 367.381 993.473 6388.86 205.302 -141.651 -101.052 0 -2381.14
-62.4463 264.55 0 0 -19.6615 -91.4706 0 -2.41393e+06 0 0 0 0 0 0 0 0
-2.40938e+06  
  
106 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MN566104.pdb  
---  
warnings | Ignored bad PDB record found on line 3926  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3927  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_5_2//MN566104.pdb  
  
Ignored bad PDB record found on line 3928  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3929  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3930  
pose -1003.85 401.899 1156.76 7932.68 239.907 -154.907 -135.941 0 -2776.8
-78.0478 284.545 0 0 -34.1555 -116.927 0 -3.7059e+06 0 0 0 0 0 0 0 0
-3.70019e+06  
  
124 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/MT377500.pdb  
---  
warnings | Ignored bad PDB record found on line 3926  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3927  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_4//MT377500.pdb  
  
Ignored bad PDB record found on line 3928  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3929  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3930  
pose -1065.51 450.568 1227.31 7661.04 240.846 -164.159 -137.301 0 -3292.41
-88.2398 292.578 0 0 -28.1659 -129.13 0 -3.72918e+06 0 0 0 0 0 0 0 0
-3.72421e+06  
  
124 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OL450365.pdb  
---  
warnings | Ignored bad PDB record found on line 3926  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3927  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_5//OL450365.pdb  
  
Ignored bad PDB record found on line 3928  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3929  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3930  
pose -1036.63 443.868 1195.34 7062.28 232.704 -161.488 -125.192 0 -2857.61
-81.638 215.057 0 0 -36.2418 -119.645 0 -3.71233e+06 0 0 0 0 0 0 0 0
-3.7076e+06  
  
124 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/ZIKVh/selected_KY/OQ661915.pdb  
---  
warnings | Ignored bad PDB record found on line 3419  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3420  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_5_2//OQ661915.pdb  
  
Ignored bad PDB record found on line 3421  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 3422  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 3423  
pose -825.377 338.598 953.262 6411.87 205.602 -152.122 -93.4969 0 -1593.46
-34.6623 165.632 0 0 -31.6973 -57.6649 0 -2.12298e+06 0 0 0 0 0 0 0 0
-2.11769e+06  
  
108 messages similar to the above omitted  
  
Chain information for KU744693.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for KX156775.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for KY765324.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for MN566104.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for MT377500.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for OL450365.pdb #6  
---  
Chain | Description  
A | No description available  
  
Chain information for OQ661915.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/OR119828.pdb

Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/MK333798.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/z_missing_represent_pdb/set_3//MK333798.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1029.27 353.369 1134.96 7430.51 251.82 -197.311 -76.6789 0 -1654.42
-72.4443 210.118 0 0 -27.823 -65.4589 0 -2.28006e+06 0 0 0 0 0 0 0 0
-2.2738e+06  
  
135 messages similar to the above omitted  
  
Summary of feedback from opening
E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/OR119828.pdb  
---  
warnings | Ignored bad PDB record found on line 4272  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 4273  
#BEGIN_POSE_ENERGIES_TABLE
/data/project/cuaim/hathaichanokc/2UTR_ver2/4_1_npz_fasta_pdb/set_3_//OR119828.pdb  
  
Ignored bad PDB record found on line 4274  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close rna_base_pair rna_base_stack rna_sugar_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 atom_pair_constraint
angle_constraint dihedral_constraint omega fa_dun p_aa_pp yhh_planarity ref
rama_prepro total  
  
Ignored bad PDB record found on line 4275  
weights 1 9 1 9 1 1 1 1.25 9 9 9 1 1 1 1 1.25 9 4 4 0.4 0.7 0.6 0.625 1 0.45
NA  
  
Ignored bad PDB record found on line 4276  
pose -1031.29 354.331 1142.81 7453.57 255.115 -191.635 -81.9594 0 -1558.49
-58.7762 234.354 0 0 -27.7766 -68.4859 0 -2.28156e+06 0 0 0 0 0 0 0 0
-2.27514e+06  
  
135 messages similar to the above omitted  
  
Chain information for MK333798.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for OR119828.pdb #9  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-9 to #1 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KU744693.pdb, chain A (#1) with KX156775.pdb, chain A (#2),
sequence alignment score = 259.1  
RMSD between 14 pruned atom pairs is 0.980 angstroms; (across all 70 pairs:
46.415)  
  
Matchmaker KU744693.pdb, chain A (#1) with KY765324.pdb, chain A (#3),
sequence alignment score = 396  
RMSD between 22 pruned atom pairs is 1.148 angstroms; (across all 103 pairs:
35.021)  
  
Matchmaker KU744693.pdb, chain A (#1) with MN566104.pdb, chain A (#4),
sequence alignment score = 429.7  
RMSD between 28 pruned atom pairs is 1.149 angstroms; (across all 120 pairs:
14.867)  
  
Matchmaker KU744693.pdb, chain A (#1) with MT377500.pdb, chain A (#5),
sequence alignment score = 429.7  
RMSD between 20 pruned atom pairs is 1.214 angstroms; (across all 120 pairs:
17.127)  
  
Matchmaker KU744693.pdb, chain A (#1) with OL450365.pdb, chain A (#6),
sequence alignment score = 429.7  
RMSD between 7 pruned atom pairs is 1.297 angstroms; (across all 120 pairs:
24.073)  
  
Matchmaker KU744693.pdb, chain A (#1) with OQ661915.pdb, chain A (#7),
sequence alignment score = 399.1  
RMSD between 25 pruned atom pairs is 1.363 angstroms; (across all 105 pairs:
40.428)  
  
Matchmaker KU744693.pdb, chain A (#1) with MK333798.pdb, chain A (#8),
sequence alignment score = 116.2  
RMSD between 4 pruned atom pairs is 0.975 angstroms; (across all 117 pairs:
48.515)  
  
Matchmaker KU744693.pdb, chain A (#1) with OR119828.pdb, chain A (#9),
sequence alignment score = 116.2  
RMSD between 3 pruned atom pairs is 1.051 angstroms; (across all 117 pairs:
42.971)  
  

> matchmaker #1,3-9 to #2 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KX156775.pdb, chain A (#2) with KU744693.pdb, chain A (#1),
sequence alignment score = 259.1  
RMSD between 14 pruned atom pairs is 0.980 angstroms; (across all 70 pairs:
46.415)  
  
Matchmaker KX156775.pdb, chain A (#2) with KY765324.pdb, chain A (#3),
sequence alignment score = 279.1  
RMSD between 9 pruned atom pairs is 0.688 angstroms; (across all 71 pairs:
38.982)  
  
Matchmaker KX156775.pdb, chain A (#2) with MN566104.pdb, chain A (#4),
sequence alignment score = 279.1  
RMSD between 9 pruned atom pairs is 1.306 angstroms; (across all 71 pairs:
36.606)  
  
Matchmaker KX156775.pdb, chain A (#2) with MT377500.pdb, chain A (#5),
sequence alignment score = 279.1  
RMSD between 8 pruned atom pairs is 0.940 angstroms; (across all 71 pairs:
35.827)  
  
Matchmaker KX156775.pdb, chain A (#2) with OL450365.pdb, chain A (#6),
sequence alignment score = 279.1  
RMSD between 10 pruned atom pairs is 0.831 angstroms; (across all 71 pairs:
44.225)  
  
Matchmaker KX156775.pdb, chain A (#2) with OQ661915.pdb, chain A (#7),
sequence alignment score = 279.1  
RMSD between 11 pruned atom pairs is 1.064 angstroms; (across all 71 pairs:
38.033)  
  
Matchmaker KX156775.pdb, chain A (#2) with MK333798.pdb, chain A (#8),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 71 pairs:
36.101)  
  
Matchmaker KX156775.pdb, chain A (#2) with OR119828.pdb, chain A (#9),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> select #9/A

4261 atoms, 4599 bonds, 133 residues, 1 model selected  

> select #1/A

3847 atoms, 4152 bonds, 120 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3/A

3339 atoms, 3605 bonds, 104 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/A

3915 atoms, 4227 bonds, 122 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #7/A

3408 atoms, 3681 bonds, 106 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/A

3915 atoms, 4227 bonds, 122 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/real_YFVh_ZIKVh_v1.cxs

——— End of log from Sat Sep 20 10:07:17 2025 ———

opened ChimeraX session  

> select protein

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> ui tool show Matchmaker

> matchmaker #6,8-9 to #2 matrix Nucleic gapExtend 10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 10  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KX156775.pdb, chain A (#2) with OL450365.pdb, chain A (#6),
sequence alignment score = 279.1  
RMSD between 10 pruned atom pairs is 0.831 angstroms; (across all 71 pairs:
44.225)  
  
Matchmaker KX156775.pdb, chain A (#2) with MK333798.pdb, chain A (#8),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 71 pairs:
36.101)  
  
Matchmaker KX156775.pdb, chain A (#2) with OR119828.pdb, chain A (#9),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> matchmaker #6,8-9 to #2 matrix Nucleic gapExtend 15

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 15  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KX156775.pdb, chain A (#2) with OL450365.pdb, chain A (#6),
sequence alignment score = 279.1  
RMSD between 10 pruned atom pairs is 0.831 angstroms; (across all 71 pairs:
44.225)  
  
Matchmaker KX156775.pdb, chain A (#2) with MK333798.pdb, chain A (#8),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 71 pairs:
36.101)  
  
Matchmaker KX156775.pdb, chain A (#2) with OR119828.pdb, chain A (#9),
sequence alignment score = 78.2  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> matchmaker #6,8-9 to #2 matrix Nucleic gapExtend 15 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 15  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker KX156775.pdb, chain A (#2) with OL450365.pdb, chain A (#6),
sequence alignment score = 279.1  
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: KX156775.pdb #2/A,
OL450365.pdb #6/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 10 pruned atom pairs is 0.831 angstroms; (across all 71 pairs:
44.225)  
  
Matchmaker KX156775.pdb, chain A (#2) with MK333798.pdb, chain A (#8),
sequence alignment score = 78.2  
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: KX156775.pdb #2/A,
MK333798.pdb #8/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 7 pruned atom pairs is 1.362 angstroms; (across all 71 pairs:
36.101)  
  
Matchmaker KX156775.pdb, chain A (#2) with OR119828.pdb, chain A (#9),
sequence alignment score = 78.2  
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: KX156775.pdb #2/A,
OR119828.pdb #9/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 7 pruned atom pairs is 0.613 angstroms; (across all 71 pairs:
41.070)  
  

> select #2/A:47

34 atoms, 36 bonds, 1 residue, 1 model selected  

> select #2/A:47-53 #9/A:95-101

444 atoms, 476 bonds, 14 residues, 2 models selected  
Seqview [ID: 3] region KX156775.pdb, chain A..OR119828.pdb, chain A [95-101]
RMSD: 0.613  
  

> select clear

> select #2/A:47

34 atoms, 36 bonds, 1 residue, 1 model selected  

> select #2/A:47-53 #9/A:95-101

444 atoms, 476 bonds, 14 residues, 2 models selected  
Seqview [ID: 3] region Cα RMSD..OR119828.pdb, chain A [95-101] RMSD: 0.613  
  

> select #6/A

3915 atoms, 4227 bonds, 122 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> undo

Undo failed, probably because structures have been modified.  

> select #8/A

4261 atoms, 4599 bonds, 133 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #9/A:125

34 atoms, 36 bonds, 1 residue, 1 model selected  

> select #9/A:125

34 atoms, 36 bonds, 1 residue, 1 model selected  

> select #2/A:71

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:57-71

487 atoms, 527 bonds, 15 residues, 1 model selected  

> select #2/A:57

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #2/A:57-71

487 atoms, 527 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #9/A:119

33 atoms, 35 bonds, 1 residue, 1 model selected  

> select #9/A:119-133

480 atoms, 517 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/real_YFVh_ZIKVh_v2.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/real_YFVh_ZIKVh_v2.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save D:/2222.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> select

5569 atoms, 6009 bonds, 174 residues, 2 models selected  

> select clear

> save
> E:/0_POSTDOC/Proj2-UTR/MS/F4_compare_structure/SET_3/YFVh/selected_MK/real_YFVh_ZIKVh_v2.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot  
'structure': self.structure,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x000002477FB653A0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002477FB653A0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000024722905370> -> <chimerax.atomic.molobject.StructureSeq object at
0x00000247317B5B50> 'MK333798.pdb, chain A': Error while saving session data
for 'tools' -> <chimerax.core.tools.Tools object at 0x000002477FB653A0> ->
<chimerax.seq-view.tool.SequenceViewer object at 0x0000024722905370> ->
<chimerax.atomic.molobject.StructureSeq object at 0x00000247317B5B50>
'MK333798.pdb, chain A'  
  
ValueError: error processing: 'tools' -> -> -> 'MK333798.pdb, chain A': Error
while saving session data for 'tools' -> -> -> 'MK333798.pdb, chain A'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\session.py", line 262, 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 512.74
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Nitro AN515-45
OS: Microsoft Windows 11 Home Single Language (Build 26100)
Memory: 33,667,739,648
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: en-US
Locale: ('en_GB', 'cp874')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Duplicate of #5560