All white coulombic

[kristen.browne@…]

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
Loading attached file and running coulombic preset.  Representation is coming out all white with a warning Hydrogen /A LYS 186 H bonded to atom that should not have hydrogens (/A LYS 186 C).  
Wasn't an issue from Chimera: https://3dprint.nih.gov/discover/3dpx-009685

Log:
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\out_15898.pdb format pdb

Summary of feedback from opening C:\Users\brownekm\Downloads\out_15898.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK --------------------PDB-to-VIPERdb MATRIX: ------------------------  
  
Ignored bad PDB record found on line 2  
REMARK -0.78508588 -0.5332578 0.3150814  
  
Ignored bad PDB record found on line 3  
REMARK 0.5156565 -0.28090696 0.80943786  
  
Ignored bad PDB record found on line 4  
REMARK -0.3431305 0.79795201 0.49551394  
  
Ignored bad PDB record found on line 5  
REMARK --------------------PDB-to-VIPERdb VECTOR: ------------------------  
  
10 messages similar to the above omitted  
  
Chain information for out_15898.pdb #1  
---  
Chain | Description  
A | No description available  
  

> preset nih3d "surface by polymer"

Using preset: NIH3D / Surface by Polymer  
Changed 1662 atom radii, 1754 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 out_15898.pdb #1  
---  
notes | No usable SEQRES records for out_15898.pdb (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A PHE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A THR 196  
Chain-final residues that are not actual C termini:  
Skipping possible acceptor with bad geometry: /A THR 23 O  
Wrong number of grandchild atoms for phi/psi acceptor /A THR 23 O  
  
Skipping possible acceptor with bad geometry: /A LYS 109 O  
Wrong number of grandchild atoms for phi/psi acceptor /A LYS 109 O  
  
Skipping possible acceptor with bad geometry: /A THR 94 O  
Wrong number of grandchild atoms for phi/psi acceptor /A THR 94 O  
  
Skipping possible acceptor with bad geometry: /A THR 131 O  
Wrong number of grandchild atoms for phi/psi acceptor /A THR 131 O  
  
Skipping possible acceptor with bad geometry: /A ASP 40 OD1  
Wrong number of grandchild atoms for phi/psi acceptor /A ASP 40 OD1  
  
32 messages similar to the above omitted  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1164, in <lambda>  
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))  
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\preset_mgr\cmd.py", line 50, in preset_cmd  
run_preset(session, cat, matches[0])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\preset_mgr\cmd.py", line 71, in run_preset  
session.presets.preset_function(category, preset)()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 60, in cb  
bi.run_provider(self.session, name, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\nih_presets\\__init__.py", line 22, in run_provider  
run_preset(session, name, mgr, **kw)  
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\nih_presets\presets.py", line 291, in run_preset  
mgr.execute(cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 88, in execute  
run(self.session, line, log=False)  
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\addh\cmd.py",
line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py",
line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py",
line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hbond.py", line 574, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\hbonds\hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 231, 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\bin\lib\site-
packages\chimerax\atomic\bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  

> open C:/Users/brownekm/Downloads/dyn1_dimer.pdb

Chain information for dyn1_dimer.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> close session

> open C:\Users\brownekm\Downloads\dyn1_dimer.pdb format pdb

Chain information for dyn1_dimer.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 24074 atom radii, 24262 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.  
7526 atoms, 5960 bonds, 1492 residues, 1 model selected  
Nothing selected  
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@ca,c4' chains palette marine:goldenrod target rs

  

> preset nih3d "surface by chain"

Using preset: NIH3D / Surface by Chain  
Changed 11998 atom radii, 12186 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 dyn1_dimer.pdb #1  
---  
warnings | Both O and OXT missing from C-terminal residue /A ASN 746; cannot
complete teminus  
Both O and OXT missing from C-terminal residue /B ASN 1492; cannot complete
teminus  
notes | No usable SEQRES records for dyn1_dimer.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for dyn1_dimer.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 747  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 746, /B ASN 1492  
Chain-final residues that are not actual C termini:  
1849 hydrogen bonds  
12074 hydrogens added  
  
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
    surface #1 enclose #1 grid 1.57911 sharp true
    rainbow #1@ca,c4' chains palette marine:goldenrod target rsa
    color zone #1 near #1 distance 20

  

> preset nih3d "surface by polymer"

Using preset: NIH3D / Surface by Polymer  
Changed 24072 atom radii, 24260 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 dyn1_dimer.pdb #1  
---  
warnings | Both O and OXT missing from C-terminal residue /A ASN 746; cannot
complete teminus  
Both O and OXT missing from C-terminal residue /B ASN 1492; cannot complete
teminus  
notes | No usable SEQRES records for dyn1_dimer.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for dyn1_dimer.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 747  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 746, /B ASN 1492  
Chain-final residues that are not actual C termini:  
1736 hydrogen bonds  
0 hydrogens added  
  
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
    surface #1 enclose #1 grid 1.88151 sharp true
    color bypolymer target ar
    color zone #1 near #1 distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 24072 atom radii, 24260 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 dyn1_dimer.pdb #1  
---  
warnings | Both O and OXT missing from C-terminal residue /A ASN 746; cannot
complete teminus  
Both O and OXT missing from C-terminal residue /B ASN 1492; cannot complete
teminus  
notes | No usable SEQRES records for dyn1_dimer.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for dyn1_dimer.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 747  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 746, /B ASN 1492  
Chain-final residues that are not actual C termini:  
1736 hydrogen bonds  
0 hydrogens added  
  

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A ILE 10  
/A ILE 23  
/A ILE 34  
/A ILE 63  
/A ILE 101  
/A ILE 115  
/A ILE 120  
/A ILE 152  
/A ILE 156  
/A ILE 171  
/A ILE 201  
/A ILE 204  
/A ILE 232  
/A ILE 242  
/A ILE 248  
/A ILE 289  
/A ILE 307  
/A ILE 344  
/A ILE 351  
/A ILE 362  
/A ILE 365  
/A ILE 388  
/A ILE 392  
/A ILE 395  
/A ILE 398  
/A ILE 412  
/A ILE 420  
/A ILE 432  
/A ILE 436  
/A ILE 459  
/A ILE 464  
/A ILE 479  
/A ILE 481  
/A ILE 494  
/A ILE 518  
/A ILE 521  
/A ILE 528  
/A ILE 531  
/A ILE 533  
/A ILE 585  
/A ILE 662  
/A ILE 672  
/A ILE 685  
/A ILE 690  
/A ILE 697  
/A ILE 741  
/A ILE 742  
/A ILE 745  
/A ASN 746  
/B ILE 756  
/B ILE 769  
/B ILE 780  
/B ILE 809  
/B ILE 847  
/B ILE 861  
/B ILE 866  
/B ILE 898  
/B ILE 902  
/B ILE 917  
/B ILE 947  
/B ILE 950  
/B ILE 978  
/B ILE 988  
/B ILE 994  
/B ILE 1035  
/B ILE 1053  
/B ILE 1090  
/B ILE 1097  
/B ILE 1108  
/B ILE 1111  
/B ILE 1134  
/B ILE 1138  
/B ILE 1141  
/B ILE 1144  
/B ILE 1158  
/B ILE 1166  
/B ILE 1178  
/B ILE 1182  
/B ILE 1205  
/B ILE 1210  
/B ILE 1225  
/B ILE 1227  
/B ILE 1240  
/B ILE 1264  
/B ILE 1267  
/B ILE 1274  
/B ILE 1277  
/B ILE 1279  
/B ILE 1331  
/B ILE 1408  
/B ILE 1418  
/B ILE 1431  
/B ILE 1436  
/B ILE 1443  
/B ILE 1487  
/B ILE 1488  
/B ILE 1491  
/B ASN 1492  

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /A ILE 742 CD  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 24072 atom radii, 24260 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 dyn1_dimer.pdb #1  
---  
warnings | Both O and OXT missing from C-terminal residue /A ASN 746; cannot
complete teminus  
Both O and OXT missing from C-terminal residue /B ASN 1492; cannot complete
teminus  
notes | No usable SEQRES records for dyn1_dimer.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for dyn1_dimer.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 747  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 746, /B ASN 1492  
Chain-final residues that are not actual C termini:  
1736 hydrogen bonds  
0 hydrogens added  
  

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A ILE 10  
/A ILE 23  
/A ILE 34  
/A ILE 63  
/A ILE 101  
/A ILE 115  
/A ILE 120  
/A ILE 152  
/A ILE 156  
/A ILE 171  
/A ILE 201  
/A ILE 204  
/A ILE 232  
/A ILE 242  
/A ILE 248  
/A ILE 289  
/A ILE 307  
/A ILE 344  
/A ILE 351  
/A ILE 362  
/A ILE 365  
/A ILE 388  
/A ILE 392  
/A ILE 395  
/A ILE 398  
/A ILE 412  
/A ILE 420  
/A ILE 432  
/A ILE 436  
/A ILE 459  
/A ILE 464  
/A ILE 479  
/A ILE 481  
/A ILE 494  
/A ILE 518  
/A ILE 521  
/A ILE 528  
/A ILE 531  
/A ILE 533  
/A ILE 585  
/A ILE 662  
/A ILE 672  
/A ILE 685  
/A ILE 690  
/A ILE 697  
/A ILE 741  
/A ILE 742  
/A ILE 745  
/A ASN 746  
/B ILE 756  
/B ILE 769  
/B ILE 780  
/B ILE 809  
/B ILE 847  
/B ILE 861  
/B ILE 866  
/B ILE 898  
/B ILE 902  
/B ILE 917  
/B ILE 947  
/B ILE 950  
/B ILE 978  
/B ILE 988  
/B ILE 994  
/B ILE 1035  
/B ILE 1053  
/B ILE 1090  
/B ILE 1097  
/B ILE 1108  
/B ILE 1111  
/B ILE 1134  
/B ILE 1138  
/B ILE 1141  
/B ILE 1144  
/B ILE 1158  
/B ILE 1166  
/B ILE 1178  
/B ILE 1182  
/B ILE 1205  
/B ILE 1210  
/B ILE 1225  
/B ILE 1227  
/B ILE 1240  
/B ILE 1264  
/B ILE 1267  
/B ILE 1274  
/B ILE 1277  
/B ILE 1279  
/B ILE 1331  
/B ILE 1408  
/B ILE 1418  
/B ILE 1431  
/B ILE 1436  
/B ILE 1443  
/B ILE 1487  
/B ILE 1488  
/B ILE 1491  
/B ASN 1492  

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /A ILE 742 CD  

> preset nih3d "surface hydrophobicity"

Using preset: NIH3D / Surface Hydrophobicity  
Changed 24072 atom radii, 24260 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 dyn1_dimer.pdb #1  
---  
warnings | Both O and OXT missing from C-terminal residue /A ASN 746; cannot
complete teminus  
Both O and OXT missing from C-terminal residue /B ASN 1492; cannot complete
teminus  
notes | No usable SEQRES records for dyn1_dimer.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for dyn1_dimer.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 747  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 746, /B ASN 1492  
Chain-final residues that are not actual C termini:  
1736 hydrogen bonds  
0 hydrogens added  
  
1492 residues, 1 surfaces, atom kd_hydrophobicity range -4.5 to 4.5  
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
    surface #1 enclose #1 grid 1.88151 sharp true
    color magenta
    color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta

  

> close session

> open C:\Users\brownekm\Downloads\dyn1_dimer.pdb format pdb

Chain information for dyn1_dimer.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 24074 atom radii, 24262 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 dyn1_dimer.pdb #1  
---  
warnings | Both O and OXT missing from C-terminal residue /A ASN 746; cannot
complete teminus  
Both O and OXT missing from C-terminal residue /B ASN 1492; cannot complete
teminus  
notes | No usable SEQRES records for dyn1_dimer.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for dyn1_dimer.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 747  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 746, /B ASN 1492  
Chain-final residues that are not actual C termini:  
1852 hydrogen bonds  
1 hydrogens added  
  

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A ILE 10  
/A ILE 23  
/A ILE 34  
/A ILE 63  
/A ILE 101  
/A ILE 115  
/A ILE 120  
/A ILE 152  
/A ILE 156  
/A ILE 171  
/A ILE 201  
/A ILE 204  
/A ILE 232  
/A ILE 242  
/A ILE 248  
/A ILE 289  
/A ILE 307  
/A ILE 344  
/A ILE 351  
/A ILE 362  
/A ILE 365  
/A ILE 388  
/A ILE 392  
/A ILE 395  
/A ILE 398  
/A ILE 412  
/A ILE 420  
/A ILE 432  
/A ILE 436  
/A ILE 459  
/A ILE 464  
/A ILE 479  
/A ILE 481  
/A ILE 494  
/A ILE 518  
/A ILE 521  
/A ILE 528  
/A ILE 531  
/A ILE 533  
/A ILE 585  
/A ILE 662  
/A ILE 672  
/A ILE 685  
/A ILE 690  
/A ILE 697  
/A ILE 741  
/A ILE 742  
/A ILE 745  
/A ASN 746  
/B ILE 756  
/B ILE 769  
/B ILE 780  
/B ILE 809  
/B ILE 847  
/B ILE 861  
/B ILE 866  
/B ILE 898  
/B ILE 902  
/B ILE 917  
/B ILE 947  
/B ILE 950  
/B ILE 978  
/B ILE 988  
/B ILE 994  
/B ILE 1035  
/B ILE 1053  
/B ILE 1090  
/B ILE 1097  
/B ILE 1108  
/B ILE 1111  
/B ILE 1134  
/B ILE 1138  
/B ILE 1141  
/B ILE 1144  
/B ILE 1158  
/B ILE 1166  
/B ILE 1178  
/B ILE 1182  
/B ILE 1205  
/B ILE 1210  
/B ILE 1225  
/B ILE 1227  
/B ILE 1240  
/B ILE 1264  
/B ILE 1267  
/B ILE 1274  
/B ILE 1277  
/B ILE 1279  
/B ILE 1331  
/B ILE 1408  
/B ILE 1418  
/B ILE 1431  
/B ILE 1436  
/B ILE 1443  
/B ILE 1487  
/B ILE 1488  
/B ILE 1491  
/B ASN 1492  

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /A ILE 398 CD  

> close session

> open C:/Users/brownekm/Downloads/CCR5.mol2

Summary of feedback from opening C:/Users/brownekm/Downloads/CCR5.mol2  
---  
warnings | line 17: ignoring section 'DICT'  
line 5076: ignoring section 'SET'  
  
Chain information for CCR5 #1  
---  
Chain | Description  
A | No description available  
  
Opened CCR5.mol2 containing 1 structures (2326 atoms, 2393 bonds)  

> preset nih3d "ribbon by chain"

Using preset: NIH3D / Ribbon by Chain  
Changed 2326 atom radii, 2393 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.  
1569 atoms, 1300 bonds, 292 residues, 1 model selected  
Nothing selected  
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@ca,c4' chains palette marine:marine target rs

  

> preset nih3d "surface by chain"

Using preset: NIH3D / Surface by Chain  
Changed 2326 atom radii, 2393 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 CCR5 #1  
---  
notes | No usable SEQRES records for CCR5 (#1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: /A PRO1 1  
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: /A GLN3 292  
290 hydrogen bonds  
/A GLN3 292 is not terminus, removing H atom from 'C'  
2393 hydrogens added  
  
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
    surface #1 enclose #1 grid 0.86661 sharp true
    rainbow #1@ca,c4' chains palette marine:marine target rsa
    color zone #1 near #1 distance 20

  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 4719 atom radii, 4786 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 CCR5 #1  
---  
notes | No usable SEQRES records for CCR5 (#1) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: /A PRO1 1  
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: /A GLN3 292  
280 hydrogen bonds  
/A GLN3 292 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1164, in <lambda>  
run(ses, "preset %s%s" % (cat, StringArg.unparse(name.lower()))))  
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\preset_mgr\cmd.py", line 50, in preset_cmd  
run_preset(session, cat, matches[0])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\preset_mgr\cmd.py", line 71, in run_preset  
session.presets.preset_function(category, preset)()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 60, in cb  
bi.run_provider(self.session, name, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\nih_presets\\__init__.py", line 22, in run_provider  
run_preset(session, name, mgr, **kw)  
File "C:\Users\brownekm\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\nih_presets\presets.py", line 291, in run_preset  
mgr.execute(cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\preset_mgr\manager.py", line 88, in execute  
run(self.session, line, log=False)  
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\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 178, in add_standard_charges  
fr = FakeRes(connected)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 727, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
ValueError: Could not come up with unique atom name in mega-residue  
  
ValueError: Could not come up with unique atom name in mega-residue  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 727, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
  
See log for complete Python traceback.  
  

> close session

> open C:/Users/brownekm/Downloads/NTD_CCD_CTD_pymol_1-coot-0_modified.pdb

Chain information for NTD_CCD_CTD_pymol_1-coot-0_modified.pdb #1  
---  
Chain | Description  
A | No description available  
  

> preset nih3d "surface coulombic"

Using preset: NIH3D / Surface Coulombic  
Changed 2124 atom radii, 2167 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
NTD_CCD_CTD_pymol_1-coot-0_modified.pdb #1  
---  
warning | Not adding hydrogens to /A GLU 48 CB because it is missing heavy-
atom bond partners  
notes | No usable SEQRES records for NTD_CCD_CTD_pymol_1-coot-0_modified.pdb
(#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A PHE 1  
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: /A ASP 270  
229 hydrogen bonds  
/A ASP 270 is not terminus, removing H atom from 'C'  
2145 hydrogens added  
  

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/A GLU 48 CD  
/A GLU 48 OE2  
/A GLU 48 OE1  
/A GLU 48 CG  

Using Amber 20 recommended default charges and atom types for standard
residues  
Hydrogen /A LYS 186 H bonded to atom that should not have hydrogens (/A LYS
186 C)  




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
File attachment: NTD_CCD_CTD_pymol_1-coot-0_modified.pdb

NTD_CCD_CTD_pymol_1-coot-0_modified.pdb​

[kristen.browne@…]

Added by email2trac

[Eric Pettersen]

The PDB has a spurious TER card in the middle of chain A, between residues 186 and 187, causing the inter-residue peptide bond to be missing (and which clearly should be there, looking at the structure). This causes hydrogens to be added that wouldn't be if the bond were there. At any rate, this failure will now be reported and the coulombic output skipped.