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#8022 closed defect (fixed)

Bad residue names from Mol2 file

Reported by:	kristen.browne@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Input/Output	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
Failure to generate the coulombic representation.  Looks like it was ok on 3DPX when generated from Chimera: https://3dprint.nih.gov/discover/3dpx-009743

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.  
  




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: CCR5.mol2

CCR5.mol2

Attachments (1)

CCR5.mol2 (305.9 KB ) - added by kristen.browne@… 3 years ago.: Added by email2trac

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Change History (4)

by kristen.browne@…, 3 years ago

Attachment:	CCR5.mol2 added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Input/Output
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Bad residue names from Mol2 file

comment:2 by Eric Pettersen, 3 years ago

I changed the Mol2 reader so that residue names like ALA19 are changed to just ALA as long as the proper SUBSTRUCTURE section is provided. After that correction there is still a problem in that residues 206 and 207 are missing their inter-residue peptide bond (and they are physically too far apart to realistically have that bond). Will investigate further tomorrow.

comment:3 by Eric Pettersen, 3 years ago

Resolution:	→ fixed
Status:	accepted → closed

The Mol2 reader wasn't adding missing-structure pseudobonds when needed. Now it does and coulombic works on this structure.

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