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#14804 closed defect (fixed)

Bad IDATM type assignment

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Structure Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open C:\Users\Dell\Desktop\ChimeraX_models\roGFP_test.cxs format session

Log from Fri Mar 22 14:44:03 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
Updating list of available bundles failed: [Errno 11001] getaddrinfo failed  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Dell/Downloads/1jc0.pdb

1jc0.pdb title:  
Crystal structure analysis of A redox-sensitive green fluorescent protein
variant In A reduced form [more info...]  
  
Chain information for 1jc0.pdb #1  
---  
Chain | Description | UniProt  
A B | green fluorescent protein | GFP_AEQVI 1-238  
C | green fluorescent protein | GFP_AEQVI 1-238  
  
Non-standard residues in 1jc0.pdb #1  
---  
CRO —
{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (peptide derived chromophore)  
  

> open C:/Users/Dell/Downloads/1jc1.pdb

1jc1.pdb title:  
Crystal structure analysis of A redox-sensitive green fluorescent protein
variant In A oxidized form [more info...]  
  
Chain information for 1jc1.pdb #2  
---  
Chain | Description | UniProt  
A | green fluorescent protein | GFP_AEQVI 1-238  
B | green fluorescent protein | GFP_AEQVI 1-238  
C | green fluorescent protein | GFP_AEQVI 1-238  
  
Non-standard residues in 1jc1.pdb #2  
---  
CRO —
{2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (peptide derived chromophore)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1jc0.pdb, chain A (#1) with 1jc1.pdb, chain A (#2), sequence
alignment score = 1190.1  
RMSD between 225 pruned atom pairs is 0.272 angstroms; (across all 225 pairs:
0.272)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1jc0.pdb, chain A (#1) with 1jc1.pdb, chain A (#2), sequence
alignment score = 1190.1  
RMSD between 225 pruned atom pairs is 0.272 angstroms; (across all 225 pairs:
0.272)  
  

> ui tool show Matchmaker

No reference and/or match structure/chain chosen  

> matchmaker #2/C to #1/C pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1jc0.pdb, chain C (#1) with 1jc1.pdb, chain C (#2), sequence
alignment score = 1149.8  
RMSD between 225 pruned atom pairs is 0.481 angstroms; (across all 225 pairs:
0.481)  
  

> transparency #1 70 All

> hide cartoons

> select #1/C

1759 atoms, 1764 bonds, 264 residues, 1 model selected  

> show sel cartoons

> select #2/C

1701 atoms, 1721 bonds, 249 residues, 1 model selected  

> transparency #1 50 All

> select ::name="CRO"

132 atoms, 138 bonds, 6 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select /C CRO

Expected a keyword  

> select /C :CRO

44 atoms, 46 bonds, 2 residues, 2 models selected  

> show sel atoms

> ui tool show "Selection Inspector"

> view sel

> select /C

3460 atoms, 3485 bonds, 513 residues, 2 models selected  

> view sel

> select clear

> select #1 /C

1759 atoms, 1764 bonds, 264 residues, 1 model selected  

> select #1 /C

1759 atoms, 1764 bonds, 264 residues, 1 model selected  

> select #2 /C

1701 atoms, 1721 bonds, 249 residues, 1 model selected  

> show sel cartoons

> select clear

> save C:/Users/Dell/Desktop/ChimeraX_models/roGFP_test.cxs

> select /C :CRO

44 atoms, 46 bonds, 2 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel makePseudobonds false color #ffaa00 relax false twoColors true
> select true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

24 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel color #ffaa00 relax false twoColors true select true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

48 hydrogen bonds found  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

48 strict hydrogen bonds found  

> view clip false

> ui tool show "Selection Inspector"

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

81 hydrogen bonds found  

> view orient

> select clear

> select #1 /C :CRO

22 atoms, 23 bonds, 1 residue, 1 model selected  

> select #1 /C :CRO

22 atoms, 23 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

15 hydrogen bonds found  

> save C:/Users/Dell/Desktop/ChimeraX_models/roGFP_test.cxs

> ui tool show H-Bonds

> hbonds sel color #ffaa00 relax false twoColors true select true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

11 hydrogen bonds found  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

11 strict hydrogen bonds found  

> view orient

> select #1 /C :147,206

11 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1 /C :147,204

12 atoms, 10 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #2 /C :147,204

12 atoms, 11 bonds, 2 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> Set transparency

Unknown command: Set transparency  

> transpaerncy

Unknown command: transpaerncy  

> transparency

Missing or invalid "percent" argument: Expected a number  

> transparency #2 70

> transparency #2 'All' 70

Missing or invalid "percent" argument: Expected a number  

> transparency #2 70 All

> transparency 70 #2 'All'

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency 0 #1 'All'

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency #1 0 All

> transparency #2 70 All

> select clear

> select /C :CRO,147,204,148,94

106 atoms, 105 bonds, 10 residues, 2 models selected  

> select /C :CRO,147,204,148,94

106 atoms, 105 bonds, 10 residues, 2 models selected  

> view orient

[Repeated 1 time(s)]

> select clear

> transparency #2 60 All

> save C:/Users/Dell/Desktop/ChimeraX_models/roGFP_test.cxs

——— End of log from Fri Mar 22 14:44:03 2024 ———

opened ChimeraX session  

> ui tool show H-Bonds

> hbonds sel color #00aaff relax false twoColors true select true reveal true

Atom specifier selects no atoms  

> select #1 /C :CRO,147,204,148,94

53 atoms, 52 bonds, 5 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00aaff relax false twoColors true select true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

27 hydrogen bonds found  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

27 strict hydrogen bonds found  

> name #1 /C :CRO,147,204,148,94

Not registering illegal selector name "#1"  

> ui tool show H-Bonds

> hbonds sel color #ffaa00 relax false twoColors true select true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

77 hydrogen bonds found  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

77 strict hydrogen bonds found  

> ui tool show "Color Actions"

> select #2 /C :CRO,147,204,148,94

53 atoms, 53 bonds, 5 residues, 1 model selected  

> color sel cyan target p

[Repeated 1 time(s)]

> select clear

> select #2 /C :CRO,147,204,148,94

53 atoms, 53 bonds, 5 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00aaff relax false twoColors true select true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

27 hydrogen bonds found  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

27 strict hydrogen bonds found  

> select #1 /C :CRO,147,204,148,94

53 atoms, 52 bonds, 5 residues, 1 model selected  

> ui tool show "Altloc Explorer"

> ui tool show H-Bonds

> hbonds sel color #00aaff relax false twoColors true select true reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

27 hydrogen bonds found  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc1.pdb #2/C GLU 172 OE2; 1jc0.pdb #1/A ARG 215 NE  

27 strict hydrogen bonds found  

> ui tool show "Dock Prep"

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
1jc0.pdb #1/A LYS 26: phi -96.1, psi 133.5 trans  
1jc0.pdb #1/A LYS 113: phi -157.9, psi 164.8 trans  
1jc0.pdb #1/A LYS 126: phi -139.7, psi 119.0 trans  
1jc0.pdb #1/A GLU 132: phi -35.5, psi -30.5 trans  
1jc0.pdb #1/A ASP 133: phi -121.0, psi 28.4 trans  
1jc0.pdb #1/A GLN 157: phi -45.1, psi -58.1 trans  
1jc0.pdb #1/A LYS 158: phi -52.5, psi -35.2 trans  
1jc0.pdb #1/A LYS 166: phi -122.6, psi 117.1 trans  
1jc0.pdb #1/A ARG 168: phi -106.1, psi 94.8 trans  
1jc0.pdb #1/A GLN 184: phi -122.1, psi 127.6 trans  
1jc0.pdb #1/A LYS 209: phi -115.7, psi 153.5 trans  
1jc0.pdb #1/A LYS 214: phi -90.3, psi -67.1 trans  
1jc0.pdb #1/A ARG 215: phi -33.7, psi 153.8 trans  
Swapping 1jc0.pdb #1/A GLY 228 to GLY  
1jc0.pdb #1/B LYS 52: phi -13.6, psi 133.3 trans  
1jc0.pdb #1/B ARG 73: phi -103.1, psi 102.5 trans  
1jc0.pdb #1/B ASP 76: phi -12.1, psi -67.1 trans  
1jc0.pdb #1/B LYS 79: phi -41.9, psi -31.1 trans  
1jc0.pdb #1/B ARG 80: phi -89.2, psi 0.5 trans  
1jc0.pdb #1/B LYS 101: phi -33.3, psi 112.6 trans  
1jc0.pdb #1/B ASP 117: phi -103.5, psi -9.4 trans  
1jc0.pdb #1/B GLU 132: phi -55.4, psi -31.0 trans  
1jc0.pdb #1/B LYS 140: phi -91.9, psi 12.5 trans  
1jc0.pdb #1/B LYS 156: phi -43.8, psi -39.0 trans  
1jc0.pdb #1/B GLN 157: phi -72.1, psi -43.8 trans  
1jc0.pdb #1/B LYS 158: phi -87.3, psi -0.1 trans  
1jc0.pdb #1/B ASN 159: phi 64.8, psi 22.8 trans  
1jc0.pdb #1/B LYS 162: phi -116.1, psi 150.4 trans  
1jc0.pdb #1/B LYS 166: phi -126.1, psi 123.0 trans  
1jc0.pdb #1/B GLU 172: phi -37.3, psi -69.0 trans  
1jc0.pdb #1/B GLN 184: phi -129.0, psi 137.2 trans  
1jc0.pdb #1/B ASN 198: phi -40.6, psi 153.3 trans  
1jc0.pdb #1/B LYS 209: phi -127.4, psi -178.5 trans  
1jc0.pdb #1/B LYS 214: phi -100.9, psi -92.6 trans  
Swapping 1jc0.pdb #1/B GLY 228 to GLY  
1jc0.pdb #1/C LYS 3: phi -66.5, psi -65.6 trans  
1jc0.pdb #1/C LEU 15: phi -137.2, psi 143.7 trans  
1jc0.pdb #1/C LYS 26: phi -96.9, psi 141.3 trans  
1jc0.pdb #1/C LYS 52: phi -6.7, psi 111.9 trans  
1jc0.pdb #1/C ASP 76: phi -35.7, psi -33.4 trans  
1jc0.pdb #1/C ARG 80: phi -61.7, psi -15.2 trans  
1jc0.pdb #1/C GLU 90: phi -78.0, psi -11.5 trans  
1jc0.pdb #1/C LYS 101: phi -55.3, psi 132.7 trans  
1jc0.pdb #1/C LYS 107: phi -118.3, psi 127.3 trans  
1jc0.pdb #1/C ARG 109: phi -124.5, psi 112.5 trans  
1jc0.pdb #1/C GLU 115: phi -110.6, psi 73.2 trans  
1jc0.pdb #1/C ARG 122: phi -120.1, psi 114.7 trans  
1jc0.pdb #1/C GLU 124: phi -110.7, psi 119.2 trans  
1jc0.pdb #1/C LYS 126: phi -125.6, psi 107.7 trans  
1jc0.pdb #1/C ASP 129: phi 77.0, psi 23.1 trans  
1jc0.pdb #1/C LYS 131: phi -113.4, psi 109.7 trans  
1jc0.pdb #1/C GLU 132: phi -46.6, psi -38.6 trans  
1jc0.pdb #1/C LYS 140: phi -94.5, psi -12.5 trans  
1jc0.pdb #1/C LYS 156: phi -30.2, psi -72.9 trans  
1jc0.pdb #1/C GLN 157: phi -65.9, psi 99.1 trans  
1jc0.pdb #1/C LYS 158: phi 150.2, psi -34.3 trans  
1jc0.pdb #1/C LYS 162: phi -111.2, psi 107.4 trans  
1jc0.pdb #1/C ASN 198: phi -85.2, psi 130.8 trans  
1jc0.pdb #1/C ASN 212: phi -106.5, psi 42.8 trans  
1jc0.pdb #1/C LYS 214: phi -72.7, psi -16.8 trans  
1jc0.pdb #1/C ILE 229: phi -151.3, psi none trans  
1jc1.pdb #2/A LYS 26: phi -98.5, psi 144.3 trans  
1jc1.pdb #2/A LYS 52: phi -48.6, psi 122.8 trans  
1jc1.pdb #2/A LYS 113: phi -162.7, psi 168.7 trans  
1jc1.pdb #2/A LYS 131: phi -75.2, psi 105.1 trans  
1jc1.pdb #2/A ASP 133: phi -108.7, psi 13.7 trans  
1jc1.pdb #2/A LYS 156: phi -59.4, psi -36.5 trans  
1jc1.pdb #2/A GLN 157: phi -73.3, psi -35.7 trans  
1jc1.pdb #2/A LYS 158: phi -82.9, psi -9.9 trans  
1jc1.pdb #2/A LYS 166: phi -123.9, psi 112.0 trans  
1jc1.pdb #2/A LYS 214: phi -73.1, psi -40.5 trans  
1jc1.pdb #2/A ILE 229: phi -77.9, psi none trans  
1jc1.pdb #2/B LYS 52: phi -34.7, psi 125.6 trans  
1jc1.pdb #2/B ARG 80: phi -78.8, psi 4.9 trans  
1jc1.pdb #2/B LYS 101: phi -48.5, psi 133.8 trans  
1jc1.pdb #2/B ASP 117: phi -96.2, psi 0.7 trans  
1jc1.pdb #2/B LYS 126: phi -109.2, psi 123.8 trans  
1jc1.pdb #2/B LYS 131: phi -97.5, psi 131.1 trans  
1jc1.pdb #2/B GLU 132: phi -40.0, psi -43.5 trans  
1jc1.pdb #2/B LYS 156: phi -41.2, psi -59.0 trans  
1jc1.pdb #2/B GLN 157: phi -60.3, psi -23.5 trans  
1jc1.pdb #2/B LYS 158: phi -108.2, psi -0.4 trans  
1jc1.pdb #2/B LYS 162: phi -123.3, psi 138.3 trans  
1jc1.pdb #2/B LYS 166: phi -123.7, psi 112.7 trans  
1jc1.pdb #2/B LYS 214: phi -95.7, psi -60.5 trans  
Swapping 1jc1.pdb #2/B GLY 228 to GLY  
1jc1.pdb #2/C LYS 3: phi -85.9, psi -50.6 trans  
1jc1.pdb #2/C THR 9: phi -36.7, psi -32.4 trans  
1jc1.pdb #2/C LEU 15: phi -132.9, psi 126.5 trans  
1jc1.pdb #2/C LYS 26: phi -107.5, psi 153.9 trans  
1jc1.pdb #2/C GLU 32: phi -127.9, psi 153.0 trans  
1jc1.pdb #2/C THR 49: phi -47.0, psi -30.7 trans  
1jc1.pdb #2/C THR 50: phi -170.2, psi 107.4 trans  
1jc1.pdb #2/C LYS 52: phi -76.9, psi 108.0 trans  
1jc1.pdb #2/C LYS 79: phi -55.6, psi -46.4 trans  
1jc1.pdb #2/C ARG 80: phi -69.4, psi 7.7 trans  
1jc1.pdb #2/C GLU 90: phi -75.8, psi -23.3 trans  
1jc1.pdb #2/C LYS 101: phi -33.2, psi 134.7 trans  
1jc1.pdb #2/C LYS 107: phi -128.6, psi 128.8 trans  
1jc1.pdb #2/C ARG 109: phi -130.3, psi 123.9 trans  
1jc1.pdb #2/C LYS 113: phi -165.1, psi 162.0 trans  
1jc1.pdb #2/C VAL 120: phi -108.8, psi 127.2 trans  
1jc1.pdb #2/C ARG 122: phi -96.6, psi 107.0 trans  
1jc1.pdb #2/C GLU 124: phi -122.0, psi 117.3 trans  
1jc1.pdb #2/C LYS 126: phi -106.3, psi 95.2 trans  
1jc1.pdb #2/C LYS 131: phi -51.5, psi 134.3 trans  
1jc1.pdb #2/C GLU 132: phi -99.0, psi 3.4 trans  
1jc1.pdb #2/C LYS 140: phi -104.3, psi -0.2 trans  
1jc1.pdb #2/C LYS 156: phi -42.2, psi -73.5 trans  
1jc1.pdb #2/C GLN 157: phi -20.0, psi -59.6 trans  
1jc1.pdb #2/C LYS 158: phi -82.8, psi -4.3 trans  
1jc1.pdb #2/C LYS 162: phi -105.0, psi 116.4 trans  
1jc1.pdb #2/C LYS 166: phi -114.0, psi 118.1 trans  
1jc1.pdb #2/C GLU 172: phi -51.9, psi -34.5 trans  
1jc1.pdb #2/C GLN 184: phi -109.6, psi 125.2 trans  
1jc1.pdb #2/C ASP 190: phi -77.0, psi -23.4 trans  
1jc1.pdb #2/C ASN 212: phi -90.9, psi 50.9 trans  
1jc1.pdb #2/C LYS 214: phi -80.2, psi -71.2 trans  
1jc1.pdb #2/C ARG 215: phi -42.7, psi 160.0 trans  
1jc1.pdb #2/C ILE 229: phi -85.1, psi none trans  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1jc0.pdb #1/A ARG 215 NE  

Applying LYS rotamer (chi angles: 67.1 -176.8 -70.5 -67.4) to 1jc0.pdb #1/A
LYS 26  
Applying LYS rotamer (chi angles: -177.0 174.8 72.6 69.1) to 1jc0.pdb #1/A LYS
113  
Applying LYS rotamer (chi angles: 59.9 175.9 72.4 -81.1) to 1jc0.pdb #1/A LYS
126  
Applying GLU rotamer (chi angles: -66.6 82.5 -3.2) to 1jc0.pdb #1/A GLU 132  
Applying ASP rotamer (chi angles: 62.3 -5.7) to 1jc0.pdb #1/A ASP 133  
Applying GLN rotamer (chi angles: -176.6 66.7 74.8) to 1jc0.pdb #1/A GLN 157  
Applying LYS rotamer (chi angles: -100.0 69.7 -96.8 -70.7) to 1jc0.pdb #1/A
LYS 158  
Applying LYS rotamer (chi angles: -76.9 86.2 96.3 -92.7) to 1jc0.pdb #1/A LYS
166  
Applying ARG rotamer (chi angles: -64.8 179.5 -175.7 -87.1) to 1jc0.pdb #1/A
ARG 168  
Applying GLN rotamer (chi angles: 64.7 -82.8 29.6) to 1jc0.pdb #1/A GLN 184  
Applying LYS rotamer (chi angles: 67.7 -89.9 167.6 60.2) to 1jc0.pdb #1/A LYS
209  
Applying LYS rotamer (chi angles: -178.5 176.8 174.2 64.9) to 1jc0.pdb #1/A
LYS 214  
Applying ARG rotamer (chi angles: -179.9 81.7 -70.3 111.4) to 1jc0.pdb #1/A
ARG 215  
Applying LYS rotamer (chi angles: -64.5 -175.6 -71.7 -68.2) to 1jc0.pdb #1/B
LYS 52  
Applying ARG rotamer (chi angles: -178.7 83.2 -78.9 -92.1) to 1jc0.pdb #1/B
ARG 73  
Applying ASP rotamer (chi angles: 61.1 -60.4) to 1jc0.pdb #1/B ASP 76  
Applying LYS rotamer (chi angles: 68.9 179.7 177.7 63.9) to 1jc0.pdb #1/B LYS
79  
Applying ARG rotamer (chi angles: -67.6 -179.3 -177.6 -85.6) to 1jc0.pdb #1/B
ARG 80  
Applying LYS rotamer (chi angles: -61.2 -68.2 -179.4 65.0) to 1jc0.pdb #1/B
LYS 101  
Applying ASP rotamer (chi angles: 62.8 -4.3) to 1jc0.pdb #1/B ASP 117  
Applying GLU rotamer (chi angles: 61.7 -85.4 -7.4) to 1jc0.pdb #1/B GLU 132  
Applying LYS rotamer (chi angles: -178.2 66.9 176.0 178.5) to 1jc0.pdb #1/B
LYS 140  
Applying LYS rotamer (chi angles: -174.7 178.4 -68.9 -68.5) to 1jc0.pdb #1/B
LYS 156  
Applying GLN rotamer (chi angles: -69.0 176.9 -24.5) to 1jc0.pdb #1/B GLN 157  
Applying LYS rotamer (chi angles: -100.0 69.7 -96.8 -70.7) to 1jc0.pdb #1/B
LYS 158  
Applying ASN rotamer (chi angles: 63.8 2.5) to 1jc0.pdb #1/B ASN 159  
Applying LYS rotamer (chi angles: -176.6 177.3 -176.1 -65.4) to 1jc0.pdb #1/B
LYS 162  
Applying LYS rotamer (chi angles: 64.2 -176.6 -177.2 -65.9) to 1jc0.pdb #1/B
LYS 166  
Applying GLU rotamer (chi angles: -177.4 177.7 57.7) to 1jc0.pdb #1/B GLU 172  
Applying GLN rotamer (chi angles: -61.3 83.4 -135.8) to 1jc0.pdb #1/B GLN 184  
Applying ASN rotamer (chi angles: 64.9 -34.2) to 1jc0.pdb #1/B ASN 198  
Applying LYS rotamer (chi angles: 60.6 -71.2 -66.8 -172.9) to 1jc0.pdb #1/B
LYS 209  
Applying LYS rotamer (chi angles: -175.1 -178.4 -70.5 -175.7) to 1jc0.pdb #1/B
LYS 214  
Applying LYS rotamer (chi angles: -100.0 69.7 -96.8 -70.7) to 1jc0.pdb #1/C
LYS 3  
Applying LEU rotamer (chi angles: -64.8 170.3) to 1jc0.pdb #1/C LEU 15  
Applying LYS rotamer (chi angles: 63.6 93.2 174.0 178.2) to 1jc0.pdb #1/C LYS
26  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 1jc0.pdb #1/C LYS
52  
Applying ASP rotamer (chi angles: -173.2 -23.7) to 1jc0.pdb #1/C ASP 76  
Applying ARG rotamer (chi angles: -70.0 178.2 -180.0 173.1) to 1jc0.pdb #1/C
ARG 80  
Applying GLU rotamer (chi angles: -175.1 175.5 -1.2) to 1jc0.pdb #1/C GLU 90  
Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to 1jc0.pdb #1/C LYS
101  
Applying LYS rotamer (chi angles: -175.8 -95.1 -71.1 178.0) to 1jc0.pdb #1/C
LYS 107  
Applying ARG rotamer (chi angles: 72.2 -92.2 179.2 91.7) to 1jc0.pdb #1/C ARG
109  
Applying GLU rotamer (chi angles: 64.6 -178.2 -0.2) to 1jc0.pdb #1/C GLU 115  
Applying ARG rotamer (chi angles: 64.5 -178.4 -67.6 171.8) to 1jc0.pdb #1/C
ARG 122  
Applying GLU rotamer (chi angles: -170.9 -83.4 -43.1) to 1jc0.pdb #1/C GLU 124  
Applying LYS rotamer (chi angles: -64.6 -65.3 -87.6 71.4) to 1jc0.pdb #1/C LYS
126  
Applying ASP rotamer (chi angles: -158.9 29.3) to 1jc0.pdb #1/C ASP 129  
Applying LYS rotamer (chi angles: 65.6 -173.6 -70.3 -174.3) to 1jc0.pdb #1/C
LYS 131  
Applying GLU rotamer (chi angles: -177.0 177.8 -1.2) to 1jc0.pdb #1/C GLU 132  
Applying LYS rotamer (chi angles: -178.1 67.9 178.5 -63.2) to 1jc0.pdb #1/C
LYS 140  
Applying LYS rotamer (chi angles: -70.2 -170.9 -71.7 -174.6) to 1jc0.pdb #1/C
LYS 156  
Applying GLN rotamer (chi angles: -66.1 82.0 43.4) to 1jc0.pdb #1/C GLN 157  
Applying LYS rotamer (chi angles: -172.5 71.1 81.2 -67.0) to 1jc0.pdb #1/C LYS
158  
Applying LYS rotamer (chi angles: -161.5 -84.3 -178.1 62.4) to 1jc0.pdb #1/C
LYS 162  
Applying ASN rotamer (chi angles: 63.5 -81.9) to 1jc0.pdb #1/C ASN 198  
Applying ASN rotamer (chi angles: -67.3 -55.5) to 1jc0.pdb #1/C ASN 212  
Applying LYS rotamer (chi angles: -89.3 65.4 -178.2 -68.0) to 1jc0.pdb #1/C
LYS 214  
Applying ILE rotamer (chi angles: -165.5 -78.0) to 1jc0.pdb #1/C ILE 229  
Applying LYS rotamer (chi angles: -177.3 177.4 178.8 -180.0) to 1jc1.pdb #2/A
LYS 26  
Applying LYS rotamer (chi angles: -82.8 74.6 176.3 67.6) to 1jc1.pdb #2/A LYS
52  
Applying LYS rotamer (chi angles: -176.3 -95.1 -71.1 178.0) to 1jc1.pdb #2/A
LYS 113  
Applying LYS rotamer (chi angles: -169.3 -83.1 -179.9 -177.4) to 1jc1.pdb #2/A
LYS 131  
Applying ASP rotamer (chi angles: -65.8 -62.4) to 1jc1.pdb #2/A ASP 133  
Applying LYS rotamer (chi angles: -70.5 179.2 -179.5 178.4) to 1jc1.pdb #2/A
LYS 156  
Applying GLN rotamer (chi angles: 63.7 -86.3 -53.8) to 1jc1.pdb #2/A GLN 157  
Applying LYS rotamer (chi angles: -172.5 71.1 81.2 -67.0) to 1jc1.pdb #2/A LYS
158  
Applying LYS rotamer (chi angles: 60.6 -111.7 -52.2 -48.0) to 1jc1.pdb #2/A
LYS 166  
Applying LYS rotamer (chi angles: -66.3 -69.8 178.1 64.4) to 1jc1.pdb #2/A LYS
214  
Applying ILE rotamer (chi angles: -165.5 -78.0) to 1jc1.pdb #2/A ILE 229  
Applying LYS rotamer (chi angles: 60.6 -71.2 -66.8 -172.9) to 1jc1.pdb #2/B
LYS 52  
Applying ARG rotamer (chi angles: -175.8 176.9 177.7 85.4) to 1jc1.pdb #2/B
ARG 80  
Applying LYS rotamer (chi angles: 67.0 -179.2 179.8 65.0) to 1jc1.pdb #2/B LYS
101  
Applying ASP rotamer (chi angles: 63.1 -3.7) to 1jc1.pdb #2/B ASP 117  
Applying LYS rotamer (chi angles: -80.1 75.3 178.2 67.6) to 1jc1.pdb #2/B LYS
126  
Applying LYS rotamer (chi angles: -178.2 91.6 -75.0 -174.6) to 1jc1.pdb #2/B
LYS 131  
Applying GLU rotamer (chi angles: -170.9 -83.6 -28.2) to 1jc1.pdb #2/B GLU 132  
Applying LYS rotamer (chi angles: -179.2 178.0 173.1 64.9) to 1jc1.pdb #2/B
LYS 156  
Applying GLN rotamer (chi angles: -174.5 175.6 6.5) to 1jc1.pdb #2/B GLN 157  
Applying LYS rotamer (chi angles: -63.9 -64.7 -87.6 70.9) to 1jc1.pdb #2/B LYS
158  
Applying LYS rotamer (chi angles: -173.7 178.4 -68.9 -68.5) to 1jc1.pdb #2/B
LYS 162  
Applying LYS rotamer (chi angles: -66.1 177.0 69.5 174.8) to 1jc1.pdb #2/B LYS
166  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 1jc1.pdb #2/B LYS
214  
Applying LYS rotamer (chi angles: -64.8 -69.3 -179.6 64.5) to 1jc1.pdb #2/C
LYS 3  
Applying THR rotamer (chi angles: -61.1) to 1jc1.pdb #2/C THR 9  
Applying LEU rotamer (chi angles: -62.9 172.4) to 1jc1.pdb #2/C LEU 15  
Applying LYS rotamer (chi angles: 63.7 93.1 173.8 178.2) to 1jc1.pdb #2/C LYS
26  
Applying GLU rotamer (chi angles: 60.4 85.9 17.2) to 1jc1.pdb #2/C GLU 32  
Applying THR rotamer (chi angles: -60.7) to 1jc1.pdb #2/C THR 49  
Applying THR rotamer (chi angles: -60.3) to 1jc1.pdb #2/C THR 50  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 1jc1.pdb #2/C LYS
52  
Applying LYS rotamer (chi angles: 64.8 93.8 174.3 178.2) to 1jc1.pdb #2/C LYS
79  
Applying ARG rotamer (chi angles: -177.0 177.8 -179.0 -86.7) to 1jc1.pdb #2/C
ARG 80  
Applying GLU rotamer (chi angles: 68.9 -176.4 53.9) to 1jc1.pdb #2/C GLU 90  
Applying LYS rotamer (chi angles: 68.0 -176.8 -70.6 -68.9) to 1jc1.pdb #2/C
LYS 101  
Applying LYS rotamer (chi angles: -64.3 -178.0 -179.5 179.6) to 1jc1.pdb #2/C
LYS 107  
Applying ARG rotamer (chi angles: 61.9 179.6 64.4 84.7) to 1jc1.pdb #2/C ARG
109  
Applying LYS rotamer (chi angles: 65.4 -174.7 -70.3 -174.3) to 1jc1.pdb #2/C
LYS 113  
Applying VAL rotamer (chi angles: -63.5) to 1jc1.pdb #2/C VAL 120  
Applying ARG rotamer (chi angles: 64.7 -177.5 -179.0 -179.0) to 1jc1.pdb #2/C
ARG 122  
Applying GLU rotamer (chi angles: -178.5 178.3 88.0) to 1jc1.pdb #2/C GLU 124  
Applying LYS rotamer (chi angles: -173.7 178.4 -68.9 -68.5) to 1jc1.pdb #2/C
LYS 126  
Applying LYS rotamer (chi angles: -63.2 -79.7 86.1 171.6) to 1jc1.pdb #2/C LYS
131  
Applying GLU rotamer (chi angles: -64.1 179.4 -3.7) to 1jc1.pdb #2/C GLU 132  
Applying LYS rotamer (chi angles: -68.2 176.1 77.6 -67.9) to 1jc1.pdb #2/C LYS
140  
Applying LYS rotamer (chi angles: 35.8 76.5 174.7 -88.1) to 1jc1.pdb #2/C LYS
156  
Applying GLN rotamer (chi angles: -67.2 81.3 -143.1) to 1jc1.pdb #2/C GLN 157  
Applying LYS rotamer (chi angles: -172.5 71.1 81.2 -67.0) to 1jc1.pdb #2/C LYS
158  
Applying LYS rotamer (chi angles: -179.0 178.9 178.8 -180.0) to 1jc1.pdb #2/C
LYS 162  
Applying LYS rotamer (chi angles: 65.4 -176.6 -177.2 -65.9) to 1jc1.pdb #2/C
LYS 166  
Applying GLU rotamer (chi angles: -176.2 65.8 48.2) to 1jc1.pdb #2/C GLU 172  
Applying GLN rotamer (chi angles: 177.7 70.0 144.0) to 1jc1.pdb #2/C GLN 184  
Applying ASP rotamer (chi angles: -168.8 31.8) to 1jc1.pdb #2/C ASP 190  
Applying ASN rotamer (chi angles: -167.4 110.6) to 1jc1.pdb #2/C ASN 212  
Applying LYS rotamer (chi angles: -178.6 177.0 174.1 64.9) to 1jc1.pdb #2/C
LYS 214  
Applying ARG rotamer (chi angles: -179.7 70.6 66.8 -169.4) to 1jc1.pdb #2/C
ARG 215  
Applying ILE rotamer (chi angles: 61.7 -80.0) to 1jc1.pdb #2/C ILE 229  
Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for 1jc0.pdb (#1) chain A; guessing termini
instead  
No usable SEQRES records for 1jc0.pdb (#1) chain B; guessing termini instead  
No usable SEQRES records for 1jc0.pdb (#1) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: 1jc0.pdb #1/A MET 1,
1jc0.pdb #1/B MET 1, 1jc0.pdb #1/C SER 2  
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: 1jc0.pdb #1/A GLY 228,
1jc0.pdb #1/B GLY 228, 1jc0.pdb #1/C ILE 229  
587 hydrogen bonds  
1jc0.pdb #1/A GLY 228 is not terminus, removing H atom from 'C'  
1jc0.pdb #1/B GLY 228 is not terminus, removing H atom from 'C'  
1jc0.pdb #1/C ILE 229 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 1jc1.pdb (#2) chain A; guessing termini instead  
No usable SEQRES records for 1jc1.pdb (#2) chain B; guessing termini instead  
No usable SEQRES records for 1jc1.pdb (#2) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: 1jc1.pdb #2/A MET 1,
1jc1.pdb #2/B MET 1, 1jc1.pdb #2/C SER 2  
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: 1jc1.pdb #2/A ILE 229,
1jc1.pdb #2/B GLY 228, 1jc1.pdb #2/C ILE 229  
623 hydrogen bonds  
1jc1.pdb #2/A ILE 229 is not terminus, removing H atom from 'C'  
1jc1.pdb #2/B GLY 228 is not terminus, removing H atom from 'C'  
1jc1.pdb #2/C ILE 229 is not terminus, removing H atom from 'C'  
10576 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CRO+LEU+VAL (net charge +0) with am1-bcc
method  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\tool.py", line 263, in add_charges  
add_nonstandard_res_charges(self.session, residues, charge, method=method)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 319, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 522, in nonstd_charge  
raise ChargeError("%s: number of electrons (%d) + formal charge (%+d) is odd;
cannot compute charges"  
chimerax.add_charge.charge.ChargeError: CRO+LEU+VAL: number of electrons (313)
+ formal charge (+0) is odd; cannot compute charges for radical species using
AM1-BCC method  
  
chimerax.add_charge.charge.ChargeError: CRO+LEU+VAL: number of electrons (313)
+ formal charge (+0) is odd; cannot compute charges for radical species using
AM1-BCC method  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 522, in nonstd_charge  
raise ChargeError("%s: number of electrons (%d) + formal charge (%+d) is odd;
cannot compute charges"  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4835
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude E7450
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,045,950,464
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-5600U CPU @ 2.60GHz
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 20 months ago

Component:	Unassigned → Structure Analysis
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Bad IDATM type assignment

1jc0 /b:cro@ca3 should be C3, not C2

comment:2 by Eric Pettersen, 20 months ago

Resolution:	→ fixed
Status:	accepted → closed

Fix: https://github.com/RBVI/ChimeraX/commit/fddde5dcf4d336bd72ce8593b85abddd8160839c

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