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Opened 23 hours ago
Closed 110 minutes ago
#19253 closed defect (not a bug)
AddH: More than 2 coplanar positions specified
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
ValueError: More than 2 coplanar positions specified!
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/laura/OneDrive/Desktop/LauraYen_2TB_stick/TARP-y7_paper/structure_comparisons/closedState/GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb
Summary of feedback from opening
C:/Users/laura/OneDrive/Desktop/LauraYen_2TB_stick/TARP-y7_paper/structure_comparisons/closedState/GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb
---
warnings | Ignored bad PDB record found on line 16112
HETATM16011 C2 SPD G**** 157.609 157.261 214.125 1.00 30.84 C
Ignored bad PDB record found on line 16113
HETATM16012 C3 SPD G**** 157.814 158.033 212.824 1.00 30.84 C
Ignored bad PDB record found on line 16114
HETATM16013 C4 SPD G**** 157.250 157.316 211.598 1.00 30.84 C
Ignored bad PDB record found on line 16115
HETATM16014 C5 SPD G**** 157.832 157.905 210.318 1.00 30.84 C
Ignored bad PDB record found on line 16116
HETATM16015 C7 SPD G**** 158.017 157.856 207.978 1.00 30.84 C
6 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (953 )
Cannot find LINK/SSBOND residue CYS (953 )
Chain information for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
E F | No description available
G H | No description available
> open
> C:/Users/laura/OneDrive/Desktop/LauraYen_2TB_stick/TARP-y7_paper/structure_comparisons/closedState/8ss3_A2-y5-CNIH2_ZK_SPD.pdb
Chain information for 8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2
---
Chain | Description
A B C D | No description available
E F | No description available
> hide atoms
> show cartoons
Computing secondary structure
> ui tool show Matchmaker
> hide #!2 models
> select #1/E#2/E
2419 atoms, 2488 bonds, 2 pseudobonds, 285 residues, 4 models selected
> hide sel & #!1 cartoons
> select #1/F#2/F
2419 atoms, 2488 bonds, 2 pseudobonds, 285 residues, 4 models selected
> hide sel & #!1 cartoons
> select #1/G
1588 atoms, 1627 bonds, 202 residues, 1 model selected
> hide sel cartoons
> select #1/H
1588 atoms, 1627 bonds, 202 residues, 1 model selected
> hide sel cartoons
Drag select of 516 residues, 4 pseudobonds
> show #!2 models
> matchmaker #!2 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb, chain A (#1)
with 8ss3_A2-y5-CNIH2_ZK_SPD.pdb, chain A (#2), sequence alignment score = 638
RMSD between 127 pruned atom pairs is 0.481 angstroms; (across all 129 pairs:
0.552)
> open
> C:/Users/laura/OneDrive/Desktop/LauraYen_2TB_stick/TARP-y7_paper/structure_comparisons/closedState/7oce_A1A2-y8-CNIH2+NBQX.pdb
Chain information for 7oce_A1A2-y8-CNIH2+NBQX.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E G | No description available
I J | No description available
> show sel cartoons
> hide sel atoms
> select clear
> show cartoons
> hide atoms
> select clear
> hide #!2 models
> hide #!3 models
> select #1/F
1166 atoms, 1203 bonds, 1 pseudobond, 140 residues, 2 models selected
> hide sel cartoons
> select #1/G
1588 atoms, 1627 bonds, 202 residues, 1 model selected
> hide sel cartoons
> select #3/I
1380 atoms, 1396 bonds, 3 pseudobonds, 190 residues, 2 models selected
> hide #!1 cartoons
> undo
> select #1/H
1588 atoms, 1627 bonds, 202 residues, 1 model selected
> hide sel cartoons
> select #1/G#3/G
2922 atoms, 3002 bonds, 364 residues, 2 models selected
> select #1/G
1588 atoms, 1627 bonds, 202 residues, 1 model selected
> select #1/E
1166 atoms, 1203 bonds, 1 pseudobond, 140 residues, 2 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> select clear
Drag select of 543 residues, 4 pseudobonds
> ui tool show Matchmaker
> show #!3 models
> matchmaker #!3 to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb, chain C (#1)
with 7oce_A1A2-y8-CNIH2+NBQX.pdb, chain C (#3), sequence alignment score =
685.8
RMSD between 133 pruned atom pairs is 0.605 angstroms; (across all 138 pairs:
1.650)
> select clear
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> hide #!3 models
> select clear
> select
57157 atoms, 58318 bonds, 34 pseudobonds, 7059 residues, 6 models selected
> show sel & #!1 cartoons
> select clear
> show #!2 models
> hide #!2 models
> show #!2 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 target m
> hide #!3 target m
> ui tool show "Side View"
> hide #!2 models
> select #1/G:45
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/G:46
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!2 models
> select add #2/A:874
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 18 atom styles
> select clear
> hide #!2 models
> coulombic #!1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_A SES
surface #1.2: minimum, -13.30, mean -0.09, maximum 19.59
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_B SES
surface #1.3: minimum, -18.48, mean -0.17, maximum 12.05
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_C SES
surface #1.4: minimum, -13.69, mean -0.08, maximum 16.76
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_D SES
surface #1.5: minimum, -29.02, mean -0.19, maximum 13.81
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_E SES
surface #1.6: minimum, -14.54, mean -1.34, maximum 7.07
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_F SES
surface #1.7: minimum, -13.72, mean -1.30, maximum 7.06
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_G SES
surface #1.8: minimum, -12.02, mean -0.22, maximum 15.78
Coulombic values for GluA1-y7-CNIH2-ZK_real_space_refined_20251028.pdb_H SES
surface #1.9: minimum, -11.98, mean -0.23, maximum 15.95
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!1 models
> show #!2 models
> coulombic #!2
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/A GLU 1035 OXT
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/C GLU 1035 OXT
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 461, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 993, in _try_finish
targets.append(_find_target(atom, at_pos, other, not is_acc, hbond_info,
finished))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 881, in _find_target
targets = bond_positions(to_atom._addh_coord, to_geom, vdw_radius(to_atom),
to_bonded,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> select clear
[Repeated 1 time(s)]
> coulombic #!2
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/A GLU 1035 OXT
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/C GLU 1035 OXT
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 461, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 993, in _try_finish
targets.append(_find_target(atom, at_pos, other, not is_acc, hbond_info,
finished))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 881, in _find_target
targets = bond_positions(to_atom._addh_coord, to_geom, vdw_radius(to_atom),
to_bonded,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> select clear
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> coulombic #!3
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLN 387
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASN 388
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 399
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 405
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 406
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASN 407
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASN 409
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLN 410
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A PHE 411
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 412
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 415
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 418
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A VAL 441
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 442
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 443
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 445
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 450
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 452
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 454
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASN 457
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 486
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLN 504
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 505
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 506
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 507
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 543
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A TYR 545
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 564
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASN 565
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 623
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 640
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 647
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 652
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 653
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 659
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 664
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 665
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A THR 668
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A MET 670
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 671
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 672
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 674
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 676
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ARG 680
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A THR 681
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 683
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 684
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A MET 686
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ILE 687
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 691
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 692
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 693
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 695
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 712
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 715
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ASP 724
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 771
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 772
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 779
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A THR 780
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A GLU 817
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A SER 818
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A LYS 819
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/A ARG 820
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B VAL 396
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B THR 399
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LEU 401
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 402
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B SER 403
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 409
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 410
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASN 411
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 413
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B MET 414
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LEU 415
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 416
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 419
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B CYS 425
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 439
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 441
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LEU 442
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASP 447
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 449
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASP 454
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASP 456
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B THR 457
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 458
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ILE 459
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 471
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASP 473
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 550
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 566
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B SER 567
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASN 569
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 627
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 634
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 637
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLN 642
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B THR 643
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 644
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASP 651
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B SER 652
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 657
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 663
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ILE 664
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASP 668
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 669
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B MET 674
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ARG 675
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B SER 676
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 678
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B SER 680
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ARG 684
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 688
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 695
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 697
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 699
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 713
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 716
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B ASP 719
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B SER 740
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B SER 741
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 761
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 770
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 781
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 782
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 783
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B GLU 821
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/B LYS 823
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLN 387
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASN 388
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 399
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 405
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 406
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASN 407
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASN 409
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLN 410
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C PHE 411
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 412
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 415
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 418
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C VAL 441
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 442
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 443
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 445
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 450
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 452
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 454
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASN 457
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 486
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLN 504
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 505
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 506
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 507
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 543
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C TYR 545
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 564
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASN 565
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 623
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 640
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 647
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 652
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 653
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 659
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 664
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 665
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C THR 668
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C MET 670
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 671
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 672
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 674
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 676
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ARG 680
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C THR 681
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 683
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 684
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C MET 686
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ILE 687
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 691
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 692
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 693
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 695
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 712
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 715
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ASP 724
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 771
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 772
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 779
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C THR 780
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C GLU 817
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C SER 818
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C LYS 819
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/C ARG 820
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D VAL 396
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D THR 399
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LEU 401
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 402
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D SER 403
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 409
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 410
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASN 411
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 413
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D MET 414
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LEU 415
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 416
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 419
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D CYS 425
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 439
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 441
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LEU 442
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASP 447
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 449
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASP 454
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASP 456
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D THR 457
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 458
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ILE 459
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 471
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASP 473
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 550
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 566
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D SER 567
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASN 569
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 627
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 634
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 637
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLN 642
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D THR 643
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 644
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASP 651
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D SER 652
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 657
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 663
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ILE 664
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASP 668
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 669
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D MET 674
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ARG 675
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D SER 676
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 678
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D SER 680
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ARG 684
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 688
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 695
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 697
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 699
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 713
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 716
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D ASP 719
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D SER 740
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D SER 741
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 761
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 770
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 781
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 782
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 783
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D GLU 821
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/D LYS 823
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ASP 32
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E GLU 33
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E THR 36
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E LYS 39
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ASN 40
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ILE 42
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ASP 43
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E GLN 44
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ASN 46
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ARG 49
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ARG 51
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E GLU 52
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ARG 53
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E ILE 57
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E SER 113
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E GLU 114
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E LYS 133
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E LEU 144
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/E SER 159
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ASP 32
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G GLU 33
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G THR 36
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G LYS 39
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ASN 40
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ILE 42
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ASP 43
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G GLN 44
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ASN 46
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ARG 49
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ARG 51
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G GLU 52
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ARG 53
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G ILE 57
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G SER 113
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G GLU 114
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G LYS 133
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G LEU 144
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/G SER 159
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I GLU 16
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LYS 17
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I PHE 29
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LEU 50
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ILE 51
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ASN 53
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I THR 54
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I PRO 78
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I GLU 93
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LEU 95
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LYS 96
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ARG 97
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LYS 102
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ASN 104
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ASP 115
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I GLU 118
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ARG 122
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I SER 148
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ARG 149
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LYS 152
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I SER 153
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LYS 154
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ARG 155
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I GLU 186
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I LYS 196
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ASN 197
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I HIS 198
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I GLU 228
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I GLU 232
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I HIS 234
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I GLN 236
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ARG 238
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I SER 239
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/I ASP 240
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J GLU 16
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LYS 17
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J PHE 29
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LEU 50
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ILE 51
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ASN 53
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J THR 54
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J PRO 78
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J GLU 93
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LEU 95
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LYS 96
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ARG 97
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LYS 102
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ASN 104
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ASP 115
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J GLU 118
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ARG 122
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J SER 148
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ARG 149
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LYS 152
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J SER 153
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LYS 154
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ARG 155
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J GLU 186
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J LYS 196
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ASN 197
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J HIS 198
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J GLU 228
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J GLU 232
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J HIS 234
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J GLN 236
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ARG 238
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J SER 239
7oce_A1A2-y8-CNIH2+NBQX.pdb #3/J ASP 240
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_A SES surface #3.2: minimum,
-11.92, mean 0.28, maximum 12.93
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_B SES surface #3.3: minimum,
-14.15, mean 0.50, maximum 15.65
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_C SES surface #3.4: minimum,
-13.42, mean 0.04, maximum 12.28
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_D SES surface #3.5: minimum,
-13.51, mean 0.30, maximum 15.43
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_E SES surface #3.6: minimum,
-21.51, mean -0.80, maximum 9.74
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_G SES surface #3.7: minimum,
-15.38, mean -0.81, maximum 9.21
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_I SES surface #3.8: minimum,
-14.05, mean -0.78, maximum 9.57
Coulombic values for 7oce_A1A2-y8-CNIH2+NBQX.pdb_J SES surface #3.9: minimum,
-14.28, mean -0.77, maximum 9.73
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> show #!2 models
> select add #2
19887 atoms, 20248 bonds, 14 pseudobonds, 2345 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> coulombic #!2
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/A GLU 1035 OXT
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/C GLU 1035 OXT
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 461, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 993, in _try_finish
targets.append(_find_target(atom, at_pos, other, not is_acc, hbond_info,
finished))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 881, in _find_target
targets = bond_positions(to_atom._addh_coord, to_geom, vdw_radius(to_atom),
to_bonded,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> coulombic #!2
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/A GLU 1035 OXT
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/C GLU 1035 OXT
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 461, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 993, in _try_finish
targets.append(_find_target(atom, at_pos, other, not is_acc, hbond_info,
finished))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 881, in _find_target
targets = bond_positions(to_atom._addh_coord, to_geom, vdw_radius(to_atom),
to_bonded,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 53320 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show #!2 cartoons
> hide #!2 atoms
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide #2.1 models
> show #2.1 models
> show #!2 cartoons
> hide #!2 surfaces
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> open
> C:/Users/laura/OneDrive/Desktop/LauraYen_2TB_stick/TARP-y7_paper/structure_comparisons/closedState/8ss3_A2-y5-CNIH2_ZK_SPD.pdb
Chain information for 8ss3_A2-y5-CNIH2_ZK_SPD.pdb #4
---
Chain | Description
A B C D | No description available
E F | No description available
> hide #!2,4 cartoons
> show #!2,4 atoms
> show #!2,4 cartoons
> hide #!2,4 atoms
> ui tool show Matchmaker
> matchmaker #!4 to #2
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8ss3_A2-y5-CNIH2_ZK_SPD.pdb, chain A (#2) with
8ss3_A2-y5-CNIH2_ZK_SPD.pdb, chain A (#4), sequence alignment score = 4647.6
RMSD between 596 pruned atom pairs is 0.000 angstroms; (across all 596 pairs:
0.000)
> hide #!4 models
> show #!4 models
> hide #!4 models
>
Incomplete command: altlocs
> :244
Unknown command: altlocs :244
> coulombic #!2
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/A GLU 1035 OXT
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/C GLU 1035 OXT
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 461, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 993, in _try_finish
targets.append(_find_target(atom, at_pos, other, not is_acc, hbond_info,
finished))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 881, in _find_target
targets = bond_positions(to_atom._addh_coord, to_geom, vdw_radius(to_atom),
to_bonded,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
> hide #2.1 models
> altLocs list
Unknown command: altLocs list
> altlocs list
9404 residues have no alternate locations
> close #4
> select add #2
19887 atoms, 20248 bonds, 14 pseudobonds, 2345 residues, 2 models selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/A GLU 1035 OXT
8ss3_A2-y5-CNIH2_ZK_SPD.pdb #2/C GLU 1035 OXT
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 215, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 402, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 420, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 339, in run
f(s)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 72, in func_plus_tip
func(cmd + " %s")(session)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 593, in run_expanded_command
run(session, cmd)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 536, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\cmd.py", line 102, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 461, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 993, in _try_finish
targets.append(_find_target(atom, at_pos, other, not is_acc, hbond_info,
finished))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 881, in _find_target
targets = bond_positions(to_atom._addh_coord, to_geom, vdw_radius(to_atom),
to_bonded,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 84, in bond_positions
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 140, in planar_pos
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
ValueError: More than 2 coplanar positions specified!
ValueError: More than 2 coplanar positions specified!
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\atomic\bond_geom.py", line 242, in angle_pos
raise ValueError("More than 2 coplanar positions specified!")
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 576.83
OpenGL renderer: NVIDIA GeForce GTX 1650 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 15 9500
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 16,913,207,296
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.7
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 2.9.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.3.4
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.3.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.8.3
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomlkit: 0.13.3
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (2)
comment:1 by , 112 minutes ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → AddH: More than 2 coplanar positions specified |
comment:2 by , 110 minutes ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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Hi Laura,
--Eric