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#8021 accepted defect

Coulombic all white

Reported by:	kristen.browne@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Surface/Binding Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202210260016 (2022-10-26 00:16:05 UTC)
Description
The attached file seems to be having trouble with the coulombic representation.  There is a warning that there is a non-standard heavy atom name.  The output representation is all white, but when looking at 3DPX for this entry https://3dprint.nih.gov/discover/3dpx-009772 that was generated by Chimera, the representation is red, white and blue as expected.  Seems like something has changed between Chimera and ChimeraX that may be resulting in a failure?

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  




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: dyn1_dimer.pdb

dyn1_dimer.pdb

Attachments (1)

dyn1_dimer.pdb (1.8 MB ) - added by kristen.browne@… 3 years ago.: Added by email2trac

Download all attachments as: .zip

Change History (7)

by kristen.browne@…, 3 years ago

Attachment:	dyn1_dimer.pdb added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Surface/Binding Analysis
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Coulombic all white

in reply to: 3 comment:2 by kristen.browne@…, 3 years ago

Eric:

I have several of this same error coming for different files, I'm guessing each with their own unique heavy atom names.  
Phil --> Do we need to handle each of these separately, or just let them fail the coulombic if they are doing non-standard things with the heavy atoms?  I've counted 6 of these so far having screened about 200 failures during reruns so far.  So it's not frequent, but certainly happening.

K

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Monday, November 14, 2022 1:31 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8021: Coulombic all white (was: ChimeraX bug report submission)

#8021: Coulombic all white
-----------------------------------------------+----------------------
          Reporter:  kristen.browne@...          |      Owner:  pett
              Type:  defect                    |     Status:  accepted
          Priority:  normal                    |  Milestone:
         Component:  Surface/Binding Analysis  |    Version:
        Resolution:                            |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+----------------------
Changes (by pett):

 * status:  new => accepted
 * component:  Unassigned => Surface/Binding Analysis
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => pett


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follow-up: 2 comment:3 by Eric Pettersen, 3 years ago

The ILEs have CD instead of the PDB-standard CD1

comment:4 by Eric Pettersen, 3 years ago

Allowing 'CD' as a synonym for 'CD1' in ILE results in another problem: Hydrogen /A CYS 427 HG1 bonded to atom that should not have hydrogens (/A CYS 427 SG)

comment:5 by Eric Pettersen, 3 years ago

Okay, also allow hydrogen attached to SG in CYS to have any name starting with 'HG' rather than just the standard plain 'HG'. This results in another error because the C terminus of this structure is protonated, and there are no charge sets for a non-physical neutral C terminus, so ultimately coulombic will be skipped for this structure despite the other fixes.

in reply to: 7 comment:6 by kristen.browne@…, 3 years ago

Looks like having the coulombic rendering skipped when it runs into any issue is going to fix a lot of the existing problems when we go to rerun.  I think that's a-ok.  We'll periodically review WHY things failed and see if it's worth fixing.

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Wednesday, November 16, 2022 2:34 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu
Subject: [EXTERNAL] Re: [ChimeraX] #8021: Coulombic all white

#8021: Coulombic all white
-----------------------------------------------+----------------------
          Reporter:  kristen.browne@...          |      Owner:  pett
              Type:  defect                    |     Status:  accepted
          Priority:  normal                    |  Milestone:
         Component:  Surface/Binding Analysis  |    Version:
        Resolution:                            |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+----------------------

Comment (by pett):

 Okay, also allow hydrogen attached to SG in CYS to have any name starting  with 'HG' rather than just the standard plain 'HG'.  This results in  another error because the C terminus of this structure is protonated, and  there are no charge sets for a non-physical neutral C terminus, so  ultimately coulombic will be skipped for this structure despite the other  fixes.

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