id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7888 Grouping model hidden kristen.browne@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.6.dev202210260016 (2022-10-26 00:16:05 UTC) Description open 2GKU change preset to ""NIH 3D>surface coulombic Works great! open 2GKU change preset to NIH3D>ribbon monochrome change preset to NIH3D>surface coulombic Structure is gone! Since the surfaces are generated AFTER the ribbons in NIH 3D, I think this is resulting in empty GLB files being output Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.6.dev202210260016 (2022-10-26) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/brownekm/Downloads/AcCAA.mol2 format mol2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\io.py"", line 196, in _make_structure residue = substid2residue[atom_data.subst_id] KeyError: None During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 457, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\\__init__.py"", line 59, in open return opener(session, data, file_name, True, True) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\io.py"", line 6, in open_mol2 p = Mol2Parser(session, stream, file_name, auto_style, atomic) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\io.py"", line 82, in __init__ self._make_structure() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\viewdockx\io.py"", line 199, in _make_structure residue = s.new_residue(""UNK"", '', atom_data.subst_id) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1817, in new_residue return f(self._c_pointer, residue_name.encode('utf-8'), chain_id.encode('utf-8'), pos, insert.encode('utf-8'), ctypes.c_void_p(0) if precedes is None else precedes._c_pointer) ctypes.ArgumentError: argument 4: : wrong type ctypes.ArgumentError: argument 4: : wrong type File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\molobject.py"", line 1817, in new_residue return f(self._c_pointer, residue_name.encode('utf-8'), chain_id.encode('utf-8'), pos, insert.encode('utf-8'), ctypes.c_void_p(0) if precedes is None else precedes._c_pointer) See log for complete Python traceback. > open 2GKU Summary of feedback from opening 2GKU fetched from pdb --- warning | Atom HO5' is not in the residue template for DT /A:1 note | Fetching compressed mmCIF 2gku from http://files.rcsb.org/download/2gku.cif 2gku title: Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 12 structures [more info...] Chain information for 2gku --- Chain | Description 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A | Human telomere DNA > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > 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 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/aabrownekm/Downloads/Basic_Webpack_x64-51.3.4843-DJP4100_Basicx64_Webpack.exe Unrecognized file suffix '.exe' > open C:/Users/brownekm/Downloads/ChimeraX_NIHPresets-1.1.1-py3-none-any.whl Unrecognized file suffix '.whl' > help help:user/preferences.html#startup > Incomplete command: toolshed > toolshed show Downloading bundle ChimeraX_NIHPresets-1.1.1-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- [notice] A new release of pip available: 22.2.2 -> 22.3 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\aabrownekm\downloads\chimerax_nihpresets-1.1.1-py3-none- any.whl Requirement already satisfied: ChimeraX-Struts>=1.0.1,~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-NIHPresets==1.1.1) (1.0.1) Requirement already satisfied: ChimeraX-PresetMgr~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-NIHPresets==1.1.1) (1.1) Requirement already satisfied: ChimeraX-Core~=1.3 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-NIHPresets==1.1.1) (1.6.dev202210260016) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- Struts>=1.0.1,~=1.0->ChimeraX-NIHPresets==1.1.1) (1.2) Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Geometry~=1.0->ChimeraX- Struts>=1.0.1,~=1.0->ChimeraX-NIHPresets==1.1.1) (1.0) Installing collected packages: ChimeraX-NIHPresets Successfully installed ChimeraX-NIHPresets-1.1.1 \--- Successfully installed ChimeraX-NIHPresets-1.1.1 Installed ChimeraX-NIHPresets (1.1.1) > preset nih3d ""surface coulombic"" Using preset: NIH3D / Surface Coulombic Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Summary of feedback from adding hydrogens to 2gku #1.1 --- notes | Termini for 2gku (#1.1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.2 --- notes | Termini for 2gku (#1.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.3 --- notes | Termini for 2gku (#1.3) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.4 --- notes | Termini for 2gku (#1.4) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.5 --- notes | Termini for 2gku (#1.5) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.6 --- notes | Termini for 2gku (#1.6) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.7 --- notes | Termini for 2gku (#1.7) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.8 --- notes | Termini for 2gku (#1.8) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.9 --- notes | Termini for 2gku (#1.9) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.10 --- notes | Termini for 2gku (#1.10) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.11 --- notes | Termini for 2gku (#1.11) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 28 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.12 --- notes | Termini for 2gku (#1.12) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 0 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues [Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum, -23.71, mean -13.48, maximum -4.18 Coulombic values for Surface #1.2 #1.2.1: minimum, -27.85, mean -13.74, maximum -2.96 Coulombic values for Surface #1.3 #1.3.1: minimum, -28.65, mean -13.83, maximum -3.69 Coulombic values for Surface #1.4 #1.4.1: minimum, -27.86, mean -13.68, maximum -3.52 Coulombic values for Surface #1.5 #1.5.1: minimum, -24.58, mean -13.66, maximum -3.87 Coulombic values for Surface #1.6 #1.6.1: minimum, -26.80, mean -13.82, maximum -3.63 Coulombic values for Surface #1.7 #1.7.1: minimum, -30.26, mean -13.76, maximum -3.62 Coulombic values for Surface #1.8 #1.8.1: minimum, -25.16, mean -13.67, maximum -4.37 Coulombic values for Surface #1.9 #1.9.1: minimum, -26.83, mean -13.67, maximum -4.11 Coulombic values for Surface #1.10 #1.10.1: minimum, -25.30, mean -13.64, maximum -3.99 Coulombic values for Surface #1.11 #1.11.1: minimum, -35.28, mean -13.72, maximum -4.02 Coulombic values for Surface #1.12 #1.12.1: minimum, -26.10, mean -13.72, maximum -3.49 Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent hide H|ligand|~(protein|nucleic-acid) ~nuc ~ribbon ~display addh #1.1 addh #1.2 addh #1.3 addh #1.4 addh #1.5 addh #1.6 addh #1.7 addh #1.8 addh #1.9 addh #1.10 addh #1.11 addh #1.12 surface #1.1 enclose #1.1 grid 0.5 sharp true surface #1.2 enclose #1.2 grid 0.5 sharp true surface #1.3 enclose #1.3 grid 0.5 sharp true surface #1.4 enclose #1.4 grid 0.5 sharp true surface #1.5 enclose #1.5 grid 0.5 sharp true surface #1.6 enclose #1.6 grid 0.5 sharp true surface #1.7 enclose #1.7 grid 0.5 sharp true surface #1.8 enclose #1.8 grid 0.5 sharp true surface #1.9 enclose #1.9 grid 0.5 sharp true surface #1.10 enclose #1.10 grid 0.5 sharp true surface #1.11 enclose #1.11 grid 0.5 sharp true surface #1.12 enclose #1.12 grid 0.5 sharp true color white coulombic surfaces #* > save 2GKU-surf-coulombic_NIH3D.glb > save C:/Users/brownekm/Desktop/2GKU-surf-coulombic_NIH3D.glb > preset nih3d ""ribbon by chain"" Using preset: NIH3D / Ribbon by Chain Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. Nothing selected [Repeated 1 time(s)]Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent delete H preset 'initial styles' cartoon nucleotides ladder radius 1.2 color white target abc color helix marine color strand firebrick color coil goldenrod color nucleic-acid forest color :A:C:G:U grape color byatom select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide) color sel carbon_grey atoms color ligand | protein & sideonly byhet atoms ~select rainbow #1.1@ca,c4' chains palette marine:marine target rs rainbow #1.2@ca,c4' chains palette marine:marine target rs rainbow #1.3@ca,c4' chains palette marine:marine target rs rainbow #1.4@ca,c4' chains palette marine:marine target rs rainbow #1.5@ca,c4' chains palette marine:marine target rs rainbow #1.6@ca,c4' chains palette marine:marine target rs rainbow #1.7@ca,c4' chains palette marine:marine target rs rainbow #1.8@ca,c4' chains palette marine:marine target rs rainbow #1.9@ca,c4' chains palette marine:marine target rs rainbow #1.10@ca,c4' chains palette marine:marine target rs rainbow #1.11@ca,c4' chains palette marine:marine target rs rainbow #1.12@ca,c4' chains palette marine:marine target rs > preset nih3d ""surface coulombic"" Using preset: NIH3D / Surface Coulombic Changed 6060 atom radii, 6816 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Summary of feedback from adding hydrogens to 2gku #1.1 --- notes | Termini for 2gku (#1.1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.2 --- notes | Termini for 2gku (#1.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.3 --- notes | Termini for 2gku (#1.3) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.4 --- notes | Termini for 2gku (#1.4) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.5 --- notes | Termini for 2gku (#1.5) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.6 --- notes | Termini for 2gku (#1.6) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.7 --- notes | Termini for 2gku (#1.7) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.8 --- notes | Termini for 2gku (#1.8) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 33 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.9 --- notes | Termini for 2gku (#1.9) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.10 --- notes | Termini for 2gku (#1.10) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.11 --- notes | Termini for 2gku (#1.11) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 28 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.12 --- notes | Termini for 2gku (#1.12) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues [Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum, -24.37, mean -13.56, maximum -4.23 Coulombic values for Surface #1.2 #1.2.1: minimum, -28.05, mean -13.74, maximum -3.00 Coulombic values for Surface #1.3 #1.3.1: minimum, -28.83, mean -13.90, maximum -3.56 Coulombic values for Surface #1.4 #1.4.1: minimum, -27.81, mean -13.73, maximum -3.43 Coulombic values for Surface #1.5 #1.5.1: minimum, -25.09, mean -13.74, maximum -3.85 Coulombic values for Surface #1.6 #1.6.1: minimum, -26.84, mean -13.95, maximum -3.76 Coulombic values for Surface #1.7 #1.7.1: minimum, -28.01, mean -13.85, maximum -3.69 Coulombic values for Surface #1.8 #1.8.1: minimum, -27.82, mean -13.71, maximum -4.12 Coulombic values for Surface #1.9 #1.9.1: minimum, -27.20, mean -13.66, maximum -4.05 Coulombic values for Surface #1.10 #1.10.1: minimum, -25.72, mean -13.65, maximum -4.08 Coulombic values for Surface #1.11 #1.11.1: minimum, -32.39, mean -13.72, maximum -4.03 Coulombic values for Surface #1.12 #1.12.1: minimum, -26.95, mean -13.76, maximum -3.62 Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent hide H|ligand|~(protein|nucleic-acid) ~nuc ~ribbon ~display addh #1.1 addh #1.2 addh #1.3 addh #1.4 addh #1.5 addh #1.6 addh #1.7 addh #1.8 addh #1.9 addh #1.10 addh #1.11 addh #1.12 surface #1.1 enclose #1.1 grid 0.5 sharp true surface #1.2 enclose #1.2 grid 0.5 sharp true surface #1.3 enclose #1.3 grid 0.5 sharp true surface #1.4 enclose #1.4 grid 0.5 sharp true surface #1.5 enclose #1.5 grid 0.5 sharp true surface #1.6 enclose #1.6 grid 0.5 sharp true surface #1.7 enclose #1.7 grid 0.5 sharp true surface #1.8 enclose #1.8 grid 0.5 sharp true surface #1.9 enclose #1.9 grid 0.5 sharp true surface #1.10 enclose #1.10 grid 0.5 sharp true surface #1.11 enclose #1.11 grid 0.5 sharp true surface #1.12 enclose #1.12 grid 0.5 sharp true color white coulombic surfaces #* > open 2GKU Summary of feedback from opening 2GKU fetched from pdb --- warning | Atom HO5' is not in the residue template for DT /A:1 2gku title: Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 12 structures [more info...] Chain information for 2gku --- Chain | Description 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A | Human telomere DNA > close session > open 2GKU Summary of feedback from opening 2GKU fetched from pdb --- warning | Atom HO5' is not in the residue template for DT /A:1 2gku title: Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 12 structures [more info...] Chain information for 2gku --- Chain | Description 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A | Human telomere DNA > preset nih3d ""surface coulombic"" Using preset: NIH3D / Surface Coulombic Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Summary of feedback from adding hydrogens to 2gku #1.1 --- notes | Termini for 2gku (#1.1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.2 --- notes | Termini for 2gku (#1.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.3 --- notes | Termini for 2gku (#1.3) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.4 --- notes | Termini for 2gku (#1.4) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.5 --- notes | Termini for 2gku (#1.5) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.6 --- notes | Termini for 2gku (#1.6) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.7 --- notes | Termini for 2gku (#1.7) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.8 --- notes | Termini for 2gku (#1.8) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.9 --- notes | Termini for 2gku (#1.9) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.10 --- notes | Termini for 2gku (#1.10) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.11 --- notes | Termini for 2gku (#1.11) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 28 hydrogen bonds 0 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.12 --- notes | Termini for 2gku (#1.12) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 0 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues [Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum, -23.71, mean -13.48, maximum -4.18 Coulombic values for Surface #1.2 #1.2.1: minimum, -27.85, mean -13.74, maximum -2.96 Coulombic values for Surface #1.3 #1.3.1: minimum, -28.65, mean -13.83, maximum -3.69 Coulombic values for Surface #1.4 #1.4.1: minimum, -27.86, mean -13.68, maximum -3.52 Coulombic values for Surface #1.5 #1.5.1: minimum, -24.58, mean -13.66, maximum -3.87 Coulombic values for Surface #1.6 #1.6.1: minimum, -26.80, mean -13.82, maximum -3.63 Coulombic values for Surface #1.7 #1.7.1: minimum, -30.26, mean -13.76, maximum -3.62 Coulombic values for Surface #1.8 #1.8.1: minimum, -25.16, mean -13.67, maximum -4.37 Coulombic values for Surface #1.9 #1.9.1: minimum, -26.83, mean -13.67, maximum -4.11 Coulombic values for Surface #1.10 #1.10.1: minimum, -25.30, mean -13.64, maximum -3.99 Coulombic values for Surface #1.11 #1.11.1: minimum, -35.28, mean -13.72, maximum -4.02 Coulombic values for Surface #1.12 #1.12.1: minimum, -26.10, mean -13.72, maximum -3.49 Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent hide H|ligand|~(protein|nucleic-acid) ~nuc ~ribbon ~display addh #1.1 addh #1.2 addh #1.3 addh #1.4 addh #1.5 addh #1.6 addh #1.7 addh #1.8 addh #1.9 addh #1.10 addh #1.11 addh #1.12 surface #1.1 enclose #1.1 grid 0.5 sharp true surface #1.2 enclose #1.2 grid 0.5 sharp true surface #1.3 enclose #1.3 grid 0.5 sharp true surface #1.4 enclose #1.4 grid 0.5 sharp true surface #1.5 enclose #1.5 grid 0.5 sharp true surface #1.6 enclose #1.6 grid 0.5 sharp true surface #1.7 enclose #1.7 grid 0.5 sharp true surface #1.8 enclose #1.8 grid 0.5 sharp true surface #1.9 enclose #1.9 grid 0.5 sharp true surface #1.10 enclose #1.10 grid 0.5 sharp true surface #1.11 enclose #1.11 grid 0.5 sharp true surface #1.12 enclose #1.12 grid 0.5 sharp true color white coulombic surfaces #* > close session > open 2GKU Summary of feedback from opening 2GKU fetched from pdb --- warning | Atom HO5' is not in the residue template for DT /A:1 2gku title: Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 12 structures [more info...] Chain information for 2gku --- Chain | Description 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A | Human telomere DNA > preset nih3d ""ribbon monochrome"" Using preset: NIH3D / Ribbon Monochrome Changed 9348 atom radii, 10104 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. Nothing selected [Repeated 1 time(s)]Assigning color attribute to 0 items Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent delete H preset 'initial styles' cartoon nucleotides ladder radius 1.2 color white target abc color helix marine color strand firebrick color coil goldenrod color nucleic-acid forest color :A:C:G:U grape color byatom select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide) color sel carbon_grey atoms color ligand | protein & sideonly byhet atoms ~select color nih_blue setattr p color nih_blue > preset nih3d ""surface coulombic"" Using preset: NIH3D / Surface Coulombic Changed 6060 atom radii, 6816 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Summary of feedback from adding hydrogens to 2gku #1.1 --- notes | Termini for 2gku (#1.1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.2 --- notes | Termini for 2gku (#1.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.3 --- notes | Termini for 2gku (#1.3) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 30 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.4 --- notes | Termini for 2gku (#1.4) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.5 --- notes | Termini for 2gku (#1.5) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.6 --- notes | Termini for 2gku (#1.6) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 29 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.7 --- notes | Termini for 2gku (#1.7) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.8 --- notes | Termini for 2gku (#1.8) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 33 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.9 --- notes | Termini for 2gku (#1.9) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.10 --- notes | Termini for 2gku (#1.10) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 32 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.11 --- notes | Termini for 2gku (#1.11) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 28 hydrogen bonds 274 hydrogens added Summary of feedback from adding hydrogens to 2gku #1.12 --- notes | Termini for 2gku (#1.12) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 31 hydrogen bonds 274 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues [Repeated 11 time(s)]Coulombic values for Surface #1.1 #1.1.1: minimum, -24.37, mean -13.56, maximum -4.23 Coulombic values for Surface #1.2 #1.2.1: minimum, -28.05, mean -13.74, maximum -3.00 Coulombic values for Surface #1.3 #1.3.1: minimum, -28.83, mean -13.90, maximum -3.56 Coulombic values for Surface #1.4 #1.4.1: minimum, -27.81, mean -13.73, maximum -3.43 Coulombic values for Surface #1.5 #1.5.1: minimum, -25.09, mean -13.74, maximum -3.85 Coulombic values for Surface #1.6 #1.6.1: minimum, -26.84, mean -13.95, maximum -3.76 Coulombic values for Surface #1.7 #1.7.1: minimum, -28.01, mean -13.85, maximum -3.69 Coulombic values for Surface #1.8 #1.8.1: minimum, -27.82, mean -13.71, maximum -4.12 Coulombic values for Surface #1.9 #1.9.1: minimum, -27.20, mean -13.66, maximum -4.05 Coulombic values for Surface #1.10 #1.10.1: minimum, -25.72, mean -13.65, maximum -4.08 Coulombic values for Surface #1.11 #1.11.1: minimum, -32.39, mean -13.72, maximum -4.03 Coulombic values for Surface #1.12 #1.12.1: minimum, -26.95, mean -13.76, maximum -3.62 Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent hide H|ligand|~(protein|nucleic-acid) ~nuc ~ribbon ~display addh #1.1 addh #1.2 addh #1.3 addh #1.4 addh #1.5 addh #1.6 addh #1.7 addh #1.8 addh #1.9 addh #1.10 addh #1.11 addh #1.12 surface #1.1 enclose #1.1 grid 0.5 sharp true surface #1.2 enclose #1.2 grid 0.5 sharp true surface #1.3 enclose #1.3 grid 0.5 sharp true surface #1.4 enclose #1.4 grid 0.5 sharp true surface #1.5 enclose #1.5 grid 0.5 sharp true surface #1.6 enclose #1.6 grid 0.5 sharp true surface #1.7 enclose #1.7 grid 0.5 sharp true surface #1.8 enclose #1.8 grid 0.5 sharp true surface #1.9 enclose #1.9 grid 0.5 sharp true surface #1.10 enclose #1.10 grid 0.5 sharp true surface #1.11 enclose #1.11 grid 0.5 sharp true surface #1.12 enclose #1.12 grid 0.5 sharp true color white coulombic surfaces #* OpenGL version: 3.3.0 NVIDIA 466.47 OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP Z4 G4 Workstation OS: Microsoft Windows 10 Enterprise (Build 19044) Memory: 137,220,087,808 MaxProcessMemory: 137,438,953,344 CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.43.2 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202210260016 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NIHPresets: 1.1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.25 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.1.1 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.2 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 prompt-toolkit: 3.0.31 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.5 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.2.1 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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 stack-data: 0.5.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.10.0 }}} " defect closed normal General Controls fixed Tom Goddard Elaine Meng all ChimeraX