AddH: Hydrogen not bonded to exactly one other atom

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/apple/Desktop/1yh3PlacedWaters (1).pdb" format pdb

No such file/path: /Users/apple/Desktop/1yh3PlacedWaters (1).pdb  

> open C1=CC(=C(C=C1C2=[O+]C3=CC(=CC(=C3C=C2)O)O)O)O fromDatabase smiles
> format smiles

Translated SMILES to 3D structure via NCI web service (SMILES:
C1=CC(=C(C=C1C2=[O+]C3=CC(=CC(=C3C=C2)O)O)O)O)  

> save /Users/apple/Desktop/441701.mol2

> open /Users/apple/Desktop/1yh3PlacedWaters.pdb

Chain information for 1yh3PlacedWaters.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> open /Users/apple/Desktop/441701.mol2

Opened 441701.mol2 containing 1 structure (31 atoms, 33 bonds)  

> open /Users/apple/Desktop/441701.mol2

Opened 441701.mol2 containing 1 structure (31 atoms, 33 bonds)  

> open /Users/apple/Desktop/441701.mol2 format mol2

Opened 441701.mol2 containing 1 structure (31 atoms, 33 bonds)  

> open /Users/apple/Desktop/441701.mol2 format mol2

Opened 441701.mol2 containing 1 structure (31 atoms, 33 bonds)  

> hide #2 models

> open /Users/apple/Desktop/441701.mol2 format mol2

Opened 441701.mol2 containing 1 structure (31 atoms, 33 bonds)  

> open 1YH3 fromDatabase pdb format mmcif

Summary of feedback from opening 1YH3 fetched from pdb  
---  
note | Fetching compressed mmCIF 1yh3 from
http://files.rcsb.org/download/1yh3.cif  
  
1yh3 title:  
Crystal structure of human CD38 extracellular domain [more info...]  
  
Chain information for 1yh3 #8  
---  
Chain | Description | UniProt  
A B | ADP-ribosyl cyclase 1 | CD38_HUMAN 45-300  
  
1yh3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> open 1YH3 format mmcif fromDatabase pdb

1yh3 title:  
Crystal structure of human CD38 extracellular domain [more info...]  
  
Chain information for 1yh3 #9  
---  
Chain | Description | UniProt  
A B | ADP-ribosyl cyclase 1 | CD38_HUMAN 45-300  
  
1yh3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide #1 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> close #7

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
1yh3PlacedWaters.pdb #2/A GLN 139: phi -149.3, psi 18.5 trans  
1yh3PlacedWaters.pdb #2/A ARG 247: phi -45.1, psi -65.0 trans  
1yh3PlacedWaters.pdb #2/A GLU 248: phi -14.7, psi 157.6 trans  
1yh3PlacedWaters.pdb #2/A ASP 249: phi -87.7, psi -29.0 trans  
1yh3PlacedWaters.pdb #2/A ARG 280: phi -130.7, psi 87.0 trans  
1yh3PlacedWaters.pdb #2/A ASN 290: phi -119.5, psi 67.6 trans  
1yh3PlacedWaters.pdb #2/A PRO 291: phi -75.1, psi 124.2 trans  
1yh3PlacedWaters.pdb #2/A GLU 292: phi 93.9, psi 176.9 trans  
1yh3PlacedWaters.pdb #2/A ASP 293: phi 55.4, psi 45.4 trans  
1yh3PlacedWaters.pdb #2/A SER 294: phi -82.0, psi 66.6 trans  
1yh3PlacedWaters.pdb #2/A SER 295: phi -59.9, psi -59.3 trans  
1yh3PlacedWaters.pdb #2/A CYS 296: phi 41.0, psi none trans  
1yh3PlacedWaters.pdb #2/B GLN 139: phi -82.5, psi 66.2 trans  
1yh3PlacedWaters.pdb #2/B ARG 140: phi -53.0, psi -19.6 trans  
1yh3PlacedWaters.pdb #2/B ASP 141: phi -74.8, psi -0.0 trans  
1yh3PlacedWaters.pdb #2/B ARG 247: phi 122.7, psi -91.5 trans  
1yh3PlacedWaters.pdb #2/B GLU 248: phi -69.5, psi -137.5 trans  
1yh3PlacedWaters.pdb #2/B ASP 249: phi 84.6, psi 43.5 trans  
1yh3PlacedWaters.pdb #2/B SER 250: phi -79.7, psi -19.1 trans  
1yh3PlacedWaters.pdb #2/B ARG 280: phi -142.5, psi 96.8 trans  
1yh3PlacedWaters.pdb #2/B ASN 290: phi -110.6, psi 79.7 trans  
1yh3PlacedWaters.pdb #2/B PRO 291: phi -47.9, psi 144.1 trans  
1yh3PlacedWaters.pdb #2/B GLU 292: phi 97.1, psi 102.0 trans  
1yh3PlacedWaters.pdb #2/B ASP 293: phi -160.9, psi 131.1 trans  
1yh3PlacedWaters.pdb #2/B SER 294: phi -67.0, psi -17.3 trans  
1yh3PlacedWaters.pdb #2/B SER 295: phi -136.1, psi 16.3 trans  
1yh3PlacedWaters.pdb #2/B CYS 296: phi -59.7, psi none trans  
1yh3 #8/A GLN 139: phi -149.3, psi 18.5 trans  
1yh3 #8/A ARG 247: phi -45.1, psi -65.0 trans  
1yh3 #8/A GLU 248: phi -14.7, psi 157.6 trans  
1yh3 #8/A ASP 249: phi -87.7, psi -29.0 trans  
1yh3 #8/A ARG 280: phi -130.7, psi 87.0 trans  
1yh3 #8/A ASN 290: phi -119.5, psi 67.6 trans  
1yh3 #8/A PRO 291: phi -75.1, psi 124.2 trans  
1yh3 #8/A GLU 292: phi 93.9, psi 176.9 trans  
1yh3 #8/A ASP 293: phi 55.4, psi 45.4 trans  
1yh3 #8/A SER 294: phi -82.0, psi 66.6 trans  
1yh3 #8/A SER 295: phi -59.9, psi -59.3 trans  
1yh3 #8/B GLN 139: phi -82.5, psi 66.2 trans  
1yh3 #8/B ARG 140: phi -53.0, psi -19.6 trans  
1yh3 #8/B ASP 141: phi -74.8, psi -0.0 trans  
1yh3 #8/B ARG 247: phi 122.7, psi -91.5 trans  
1yh3 #8/B GLU 248: phi -69.5, psi -137.5 trans  
1yh3 #8/B ASP 249: phi 84.6, psi 43.5 trans  
1yh3 #8/B SER 250: phi -79.7, psi -19.1 trans  
1yh3 #8/B ARG 280: phi -142.5, psi 96.8 trans  
1yh3 #8/B ASN 290: phi -110.6, psi 79.7 trans  
1yh3 #8/B PRO 291: phi -47.9, psi 144.1 trans  
1yh3 #8/B GLU 292: phi 97.1, psi 102.0 trans  
1yh3 #8/B ASP 293: phi -160.9, psi 131.1 trans  
1yh3 #8/B SER 294: phi -67.0, psi -17.3 trans  
1yh3 #8/B SER 295: phi -136.1, psi 16.3 trans  
1yh3 #9/A GLN 139: phi -149.3, psi 18.5 trans  
1yh3 #9/A ARG 247: phi -45.1, psi -65.0 trans  
1yh3 #9/A GLU 248: phi -14.7, psi 157.6 trans  
1yh3 #9/A ASP 249: phi -87.7, psi -29.0 trans  
1yh3 #9/A ARG 280: phi -130.7, psi 87.0 trans  
1yh3 #9/A ASN 290: phi -119.5, psi 67.6 trans  
1yh3 #9/A PRO 291: phi -75.1, psi 124.2 trans  
1yh3 #9/A GLU 292: phi 93.9, psi 176.9 trans  
1yh3 #9/A ASP 293: phi 55.4, psi 45.4 trans  
1yh3 #9/A SER 294: phi -82.0, psi 66.6 trans  
1yh3 #9/A SER 295: phi -59.9, psi -59.3 trans  
1yh3 #9/B GLN 139: phi -82.5, psi 66.2 trans  
1yh3 #9/B ARG 140: phi -53.0, psi -19.6 trans  
1yh3 #9/B ASP 141: phi -74.8, psi -0.0 trans  
1yh3 #9/B ARG 247: phi 122.7, psi -91.5 trans  
1yh3 #9/B GLU 248: phi -69.5, psi -137.5 trans  
1yh3 #9/B ASP 249: phi 84.6, psi 43.5 trans  
1yh3 #9/B SER 250: phi -79.7, psi -19.1 trans  
1yh3 #9/B ARG 280: phi -142.5, psi 96.8 trans  
1yh3 #9/B ASN 290: phi -110.6, psi 79.7 trans  
1yh3 #9/B PRO 291: phi -47.9, psi 144.1 trans  
1yh3 #9/B GLU 292: phi 97.1, psi 102.0 trans  
1yh3 #9/B ASP 293: phi -160.9, psi 131.1 trans  
1yh3 #9/B SER 294: phi -67.0, psi -17.3 trans  
1yh3 #9/B SER 295: phi -136.1, psi 16.3 trans  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1yh3PlacedWaters.pdb #2/B PRO 291 N; 1yh3PlacedWaters.pdb #2/A
PRO 291 N; 1yh3 #8/B PRO 291 N; 1yh3 #9/A PRO 291 N; 1yh3 #8/A PRO 291 N; 1yh3
#9/B PRO 291 N  

Applying GLN rotamer (chi angles: -61.9 -64.7 -49.3) to 1yh3PlacedWaters.pdb
#2/A GLN 139  
Applying ARG rotamer (chi angles: -87.2 79.2 -84.3 -75.1) to
1yh3PlacedWaters.pdb #2/A ARG 247  
Applying GLU rotamer (chi angles: -66.7 179.1 -6.3) to 1yh3PlacedWaters.pdb
#2/A GLU 248  
Applying ASP rotamer (chi angles: -64.7 -52.5) to 1yh3PlacedWaters.pdb #2/A
ASP 249  
Applying ARG rotamer (chi angles: -67.1 -86.2 67.9 -109.4) to
1yh3PlacedWaters.pdb #2/A ARG 280  
Applying ASN rotamer (chi angles: 63.0 13.7) to 1yh3PlacedWaters.pdb #2/A ASN
290  
Applying PRO rotamer (chi angles: 28.0 -31.7) to 1yh3PlacedWaters.pdb #2/A PRO
291  
Applying GLU rotamer (chi angles: -66.3 179.4 -6.2) to 1yh3PlacedWaters.pdb
#2/A GLU 292  
Applying ASP rotamer (chi angles: -64.0 -35.7) to 1yh3PlacedWaters.pdb #2/A
ASP 293  
Applying SER rotamer (chi angles: -63.6) to 1yh3PlacedWaters.pdb #2/A SER 294  
Applying SER rotamer (chi angles: 63.6) to 1yh3PlacedWaters.pdb #2/A SER 295  
Applying CYS rotamer (chi angles: 63.7) to 1yh3PlacedWaters.pdb #2/A CYS 296  
Applying GLN rotamer (chi angles: -178.6 66.4 52.5) to 1yh3PlacedWaters.pdb
#2/B GLN 139  
Applying ARG rotamer (chi angles: -71.5 -173.3 -72.5 106.3) to
1yh3PlacedWaters.pdb #2/B ARG 140  
Applying ASP rotamer (chi angles: -69.9 -46.2) to 1yh3PlacedWaters.pdb #2/B
ASP 141  
Applying ARG rotamer (chi angles: -174.7 177.9 -63.0 107.3) to
1yh3PlacedWaters.pdb #2/B ARG 247  
Applying GLU rotamer (chi angles: -66.9 179.0 -6.7) to 1yh3PlacedWaters.pdb
#2/B GLU 248  
Applying ASP rotamer (chi angles: -64.5 55.6) to 1yh3PlacedWaters.pdb #2/B ASP
249  
Applying SER rotamer (chi angles: 67.5) to 1yh3PlacedWaters.pdb #2/B SER 250  
Applying ARG rotamer (chi angles: -73.0 85.6 61.5 85.9) to
1yh3PlacedWaters.pdb #2/B ARG 280  
Applying ASN rotamer (chi angles: -64.4 -112.2) to 1yh3PlacedWaters.pdb #2/B
ASN 290  
Applying PRO rotamer (chi angles: -29.1 38.5) to 1yh3PlacedWaters.pdb #2/B PRO
291  
Applying GLU rotamer (chi angles: -66.7 179.1 -6.3) to 1yh3PlacedWaters.pdb
#2/B GLU 292  
Applying ASP rotamer (chi angles: -170.7 -39.1) to 1yh3PlacedWaters.pdb #2/B
ASP 293  
Applying SER rotamer (chi angles: -65.6) to 1yh3PlacedWaters.pdb #2/B SER 294  
Applying SER rotamer (chi angles: -61.5) to 1yh3PlacedWaters.pdb #2/B SER 295  
Applying CYS rotamer (chi angles: 63.7) to 1yh3PlacedWaters.pdb #2/B CYS 296  
Applying GLN rotamer (chi angles: -64.4 179.0 -26.5) to 1yh3 #8/A GLN 139  
Applying ARG rotamer (chi angles: -87.2 79.2 -84.3 -75.1) to 1yh3 #8/A ARG 247  
Applying GLU rotamer (chi angles: -66.7 179.1 -6.3) to 1yh3 #8/A GLU 248  
Applying ASP rotamer (chi angles: -170.8 60.7) to 1yh3 #8/A ASP 249  
Applying ARG rotamer (chi angles: -67.1 -86.2 67.9 -109.4) to 1yh3 #8/A ARG
280  
Applying ASN rotamer (chi angles: 63.0 13.7) to 1yh3 #8/A ASN 290  
Applying PRO rotamer (chi angles: 28.0 -31.7) to 1yh3 #8/A PRO 291  
Applying GLU rotamer (chi angles: -66.3 179.4 -6.2) to 1yh3 #8/A GLU 292  
Applying ASP rotamer (chi angles: -163.8 48.9) to 1yh3 #8/A ASP 293  
Applying SER rotamer (chi angles: -177.5) to 1yh3 #8/A SER 294  
Applying SER rotamer (chi angles: 63.6) to 1yh3 #8/A SER 295  
Applying GLN rotamer (chi angles: -175.2 177.3 66.1) to 1yh3 #8/B GLN 139  
Applying ARG rotamer (chi angles: -71.5 -173.3 -72.5 106.3) to 1yh3 #8/B ARG
140  
Applying ASP rotamer (chi angles: -69.9 -46.2) to 1yh3 #8/B ASP 141  
Applying ARG rotamer (chi angles: -174.7 177.9 -63.0 107.3) to 1yh3 #8/B ARG
247  
Applying GLU rotamer (chi angles: -66.9 179.0 -6.7) to 1yh3 #8/B GLU 248  
Applying ASP rotamer (chi angles: -64.5 55.6) to 1yh3 #8/B ASP 249  
Applying SER rotamer (chi angles: -179.5) to 1yh3 #8/B SER 250  
Applying ARG rotamer (chi angles: -73.0 85.6 61.5 85.9) to 1yh3 #8/B ARG 280  
Applying ASN rotamer (chi angles: -174.6 -2.5) to 1yh3 #8/B ASN 290  
Applying PRO rotamer (chi angles: -29.1 38.5) to 1yh3 #8/B PRO 291  
Applying GLU rotamer (chi angles: -66.7 179.1 -6.3) to 1yh3 #8/B GLU 292  
Applying ASP rotamer (chi angles: -170.7 -39.1) to 1yh3 #8/B ASP 293  
Applying SER rotamer (chi angles: -178.9) to 1yh3 #8/B SER 294  
Applying SER rotamer (chi angles: -178.9) to 1yh3 #8/B SER 295  
Applying GLN rotamer (chi angles: -64.4 179.0 -26.5) to 1yh3 #9/A GLN 139  
Applying ARG rotamer (chi angles: -87.2 79.2 -84.3 -75.1) to 1yh3 #9/A ARG 247  
Applying GLU rotamer (chi angles: -66.7 179.1 -6.3) to 1yh3 #9/A GLU 248  
Applying ASP rotamer (chi angles: -170.8 60.7) to 1yh3 #9/A ASP 249  
Applying ARG rotamer (chi angles: -67.1 -86.2 67.9 -109.4) to 1yh3 #9/A ARG
280  
Applying ASN rotamer (chi angles: 63.0 13.7) to 1yh3 #9/A ASN 290  
Applying PRO rotamer (chi angles: 28.0 -31.7) to 1yh3 #9/A PRO 291  
Applying GLU rotamer (chi angles: -66.3 179.4 -6.2) to 1yh3 #9/A GLU 292  
Applying ASP rotamer (chi angles: -163.8 48.9) to 1yh3 #9/A ASP 293  
Applying SER rotamer (chi angles: -177.5) to 1yh3 #9/A SER 294  
Applying SER rotamer (chi angles: 63.6) to 1yh3 #9/A SER 295  
Applying GLN rotamer (chi angles: -175.2 177.3 66.1) to 1yh3 #9/B GLN 139  
Applying ARG rotamer (chi angles: -71.5 -173.3 -72.5 106.3) to 1yh3 #9/B ARG
140  
Applying ASP rotamer (chi angles: -69.9 -46.2) to 1yh3 #9/B ASP 141  
Applying ARG rotamer (chi angles: -174.7 177.9 -63.0 107.3) to 1yh3 #9/B ARG
247  
Applying GLU rotamer (chi angles: -66.9 179.0 -6.7) to 1yh3 #9/B GLU 248  
Applying ASP rotamer (chi angles: -64.5 55.6) to 1yh3 #9/B ASP 249  
Applying SER rotamer (chi angles: -179.5) to 1yh3 #9/B SER 250  
Applying ARG rotamer (chi angles: -73.0 85.6 61.5 85.9) to 1yh3 #9/B ARG 280  
Applying ASN rotamer (chi angles: -174.6 -2.5) to 1yh3 #9/B ASN 290  
Applying PRO rotamer (chi angles: -29.1 38.5) to 1yh3 #9/B PRO 291  
Applying GLU rotamer (chi angles: -66.7 179.1 -6.3) to 1yh3 #9/B GLU 292  
Applying ASP rotamer (chi angles: -170.7 -39.1) to 1yh3 #9/B ASP 293  
Applying SER rotamer (chi angles: -178.9) to 1yh3 #9/B SER 294  
Applying SER rotamer (chi angles: -178.9) to 1yh3 #9/B SER 295  
Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
No usable SEQRES records for 1yh3PlacedWaters.pdb (#2) chain A; guessing
termini instead  
No usable SEQRES records for 1yh3PlacedWaters.pdb (#2) chain B; guessing
termini instead  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 1yh3PlacedWaters.pdb
#2/A ARG 45, 1yh3PlacedWaters.pdb #2/B ARG 45  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1yh3PlacedWaters.pdb #2/A
CYS 296, 1yh3PlacedWaters.pdb #2/B CYS 296  
446 hydrogen bonds  
1yh3PlacedWaters.pdb #2/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3PlacedWaters.pdb #2/B CYS 296 is not terminus, removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Termini for 1yh3 (#8) chain A determined from SEQRES records  
Termini for 1yh3 (#8) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: 1yh3 #8/A ARG 45, 1yh3 #8/B
ARG 45  
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: 1yh3 #8/A CYS 296, 1yh3
#8/B CYS 296  
453 hydrogen bonds  
1yh3 #8/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3 #8/B CYS 296 is not terminus, removing H atom from 'C'  
Termini for 1yh3 (#9) chain A determined from SEQRES records  
Termini for 1yh3 (#9) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: 1yh3 #9/A ARG 45, 1yh3 #9/B
ARG 45  
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: 1yh3 #9/A CYS 296, 1yh3
#9/B CYS 296  
453 hydrogen bonds  
1yh3 #9/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3 #9/B CYS 296 is not terminus, removing H atom from 'C'  
8081 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 UNL (net charge +1) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/wl/s0fmryxn2s7fj37c7tr9jg3h0000gn/T/tmpddgmdyzw/ante.in.mol2 -fi
mol2 -o
/var/folders/wl/s0fmryxn2s7fj37c7tr9jg3h0000gn/T/tmpddgmdyzw/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(/var/folders/wl/s0fmryxn2s7fj37c7tr9jg3h0000gn/T/tmpddgmdyzw/ante.in.mol2);
atoms read (31), bonds read (33).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) ``  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `Info: Total number of electrons: 140; net charge: 1`  
(UNL) ``  
(UNL) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(UNL) ``  
(UNL) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNL) ``  
Charges for residue UNL determined  
Dock prep finished  

> save /Users/apple/Downloads/1YH3_docked.pdb

> save /Users/apple/Downloads/1YH3.pdb

> hide #8 models

> hide #9 models

> show #8 models

> hide #8 models

> show #9 models

> hide #9 models

> show #8 models

> hide #8 models

> show #6 models

> hide #6 models

> show #1 models

> hide #1 models

> show #2 models

> hide #2 models

> show #8 models

> save /Users/apple/Downloads/1YH3(1).pdb

> save /Users/apple/Downloads/1YH3.pdb

> open 1YH3 fromDatabase pdb format mmcif

1yh3 title:  
Crystal structure of human CD38 extracellular domain [more info...]  
  
Chain information for 1yh3 #7  
---  
Chain | Description | UniProt  
A B | ADP-ribosyl cyclase 1 | CD38_HUMAN 45-300  
  
1yh3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> save /Users/apple/Downloads/1YHS_please.pdb

> save /1YH3_pls.pdb

Cannot save '/1YH3_pls.pdb': Unable to open file '/1YH3_pls.pdb' for writing  

> open /Users/apple/Downloads/1b6m.pdb

Summary of feedback from opening /Users/apple/Downloads/1b6m.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 7/ 8/ 9 13:54:51 CREATED BY USER: aurelien  
  
Chain information for 1b6m.pdb #10  
---  
Chain | Description  
? | No description available  
  

> hide #7 models

> hide #8 models

> hide #!10 models

> show #6 models

> hide #6 models

> show #7 models

> hide #7 models

> show #8 models

> save /Users/apple/Desktop/1YH3_yes.pdb

> open 1YH3 fromDatabase pdb format mmcif

1yh3 title:  
Crystal structure of human CD38 extracellular domain [more info...]  
  
Chain information for 1yh3 #11  
---  
Chain | Description | UniProt  
A B | ADP-ribosyl cyclase 1 | CD38_HUMAN 45-300  
  
1yh3 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> save /Users/apple/Desktop/1YH3_plspls.pdb

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
1yh3PlacedWaters.pdb #2/A CYS 296: phi 41.0, psi none trans  
1yh3PlacedWaters.pdb #2/B CYS 296: phi -59.7, psi none trans  
1yh3 #7/A GLN 139: phi -149.3, psi 18.5 trans  
1yh3 #7/A ARG 247: phi -45.1, psi -65.0 trans  
1yh3 #7/A GLU 248: phi -14.7, psi 157.6 trans  
1yh3 #7/A ASP 249: phi -87.7, psi -29.0 trans  
1yh3 #7/A ARG 280: phi -130.7, psi 87.0 trans  
1yh3 #7/A ASN 290: phi -119.5, psi 67.6 trans  
1yh3 #7/A PRO 291: phi -75.1, psi 124.2 trans  
1yh3 #7/A GLU 292: phi 93.9, psi 176.9 trans  
1yh3 #7/A ASP 293: phi 55.4, psi 45.4 trans  
1yh3 #7/A SER 294: phi -82.0, psi 66.6 trans  
1yh3 #7/A SER 295: phi -59.9, psi -59.3 trans  
1yh3 #7/B GLN 139: phi -82.5, psi 66.2 trans  
1yh3 #7/B ARG 140: phi -53.0, psi -19.6 trans  
1yh3 #7/B ASP 141: phi -74.8, psi -0.0 trans  
1yh3 #7/B ARG 247: phi 122.7, psi -91.5 trans  
1yh3 #7/B GLU 248: phi -69.5, psi -137.5 trans  
1yh3 #7/B ASP 249: phi 84.6, psi 43.5 trans  
1yh3 #7/B SER 250: phi -79.7, psi -19.1 trans  
1yh3 #7/B ARG 280: phi -142.5, psi 96.8 trans  
1yh3 #7/B ASN 290: phi -110.6, psi 79.7 trans  
1yh3 #7/B PRO 291: phi -47.9, psi 144.1 trans  
1yh3 #7/B GLU 292: phi 97.1, psi 102.0 trans  
1yh3 #7/B ASP 293: phi -160.9, psi 131.1 trans  
1yh3 #7/B SER 294: phi -67.0, psi -17.3 trans  
1yh3 #7/B SER 295: phi -136.1, psi 16.3 trans  
1b6m.pdb #10/? PRO 1: phi none, psi 168.2 trans  
1b6m.pdb #10/? PHE 99: phi -159.9, psi none trans  
1yh3 #11/A GLN 139: phi -149.3, psi 18.5 trans  
1yh3 #11/A ARG 247: phi -45.1, psi -65.0 trans  
1yh3 #11/A GLU 248: phi -14.7, psi 157.6 trans  
1yh3 #11/A ASP 249: phi -87.7, psi -29.0 trans  
1yh3 #11/A ARG 280: phi -130.7, psi 87.0 trans  
1yh3 #11/A ASN 290: phi -119.5, psi 67.6 trans  
1yh3 #11/A PRO 291: phi -75.1, psi 124.2 trans  
1yh3 #11/A GLU 292: phi 93.9, psi 176.9 trans  
1yh3 #11/A ASP 293: phi 55.4, psi 45.4 trans  
1yh3 #11/A SER 294: phi -82.0, psi 66.6 trans  
1yh3 #11/A SER 295: phi -59.9, psi -59.3 trans  
1yh3 #11/B GLN 139: phi -82.5, psi 66.2 trans  
1yh3 #11/B ARG 140: phi -53.0, psi -19.6 trans  
1yh3 #11/B ASP 141: phi -74.8, psi -0.0 trans  
1yh3 #11/B ARG 247: phi 122.7, psi -91.5 trans  
1yh3 #11/B GLU 248: phi -69.5, psi -137.5 trans  
1yh3 #11/B ASP 249: phi 84.6, psi 43.5 trans  
1yh3 #11/B SER 250: phi -79.7, psi -19.1 trans  
1yh3 #11/B ARG 280: phi -142.5, psi 96.8 trans  
1yh3 #11/B ASN 290: phi -110.6, psi 79.7 trans  
1yh3 #11/B PRO 291: phi -47.9, psi 144.1 trans  
1yh3 #11/B GLU 292: phi 97.1, psi 102.0 trans  
1yh3 #11/B ASP 293: phi -160.9, psi 131.1 trans  
1yh3 #11/B SER 294: phi -67.0, psi -17.3 trans  
1yh3 #11/B SER 295: phi -136.1, psi 16.3 trans  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 1yh3 #7/A PRO 291 N; 1yh3 #11/A PRO 291 N; 1yh3 #11/B PRO 291
N; 1yh3 #7/B PRO 291 N  

Applying CYS rotamer (chi angles: 63.7) to 1yh3PlacedWaters.pdb #2/A CYS 296  
Applying CYS rotamer (chi angles: 63.7) to 1yh3PlacedWaters.pdb #2/B CYS 296  
Applying GLN rotamer (chi angles: -171.4 -83.6 145.1) to 1yh3 #7/A GLN 139  
Applying ARG rotamer (chi angles: -178.0 -92.7 178.2 -84.3) to 1yh3 #7/A ARG
247  
Applying GLU rotamer (chi angles: 66.6 -84.1 16.8) to 1yh3 #7/A GLU 248  
Applying ASP rotamer (chi angles: 60.3 -45.5) to 1yh3 #7/A ASP 249  
Applying ARG rotamer (chi angles: 69.0 -77.0 -66.6 163.4) to 1yh3 #7/A ARG 280  
Applying ASN rotamer (chi angles: -63.0 81.5) to 1yh3 #7/A ASN 290  
Applying PRO rotamer (chi angles: -17.2 32.6) to 1yh3 #7/A PRO 291  
Applying GLU rotamer (chi angles: -177.7 65.6 78.7) to 1yh3 #7/A GLU 292  
Applying ASP rotamer (chi angles: -64.0 -9.5) to 1yh3 #7/A ASP 293  
Applying SER rotamer (chi angles: 54.0) to 1yh3 #7/A SER 294  
Applying SER rotamer (chi angles: -65.7) to 1yh3 #7/A SER 295  
Applying GLN rotamer (chi angles: -61.4 -66.0 58.6) to 1yh3 #7/B GLN 139  
Applying ARG rotamer (chi angles: 72.0 -81.7 -164.0 -170.2) to 1yh3 #7/B ARG
140  
Applying ASP rotamer (chi angles: -167.4 1.1) to 1yh3 #7/B ASP 141  
Applying ARG rotamer (chi angles: -84.4 70.3 175.4 175.2) to 1yh3 #7/B ARG 247  
Applying GLU rotamer (chi angles: 66.6 -84.2 17.2) to 1yh3 #7/B GLU 248  
Applying ASP rotamer (chi angles: 62.9 61.0) to 1yh3 #7/B ASP 249  
Applying SER rotamer (chi angles: -64.9) to 1yh3 #7/B SER 250  
Applying ARG rotamer (chi angles: -177.2 177.6 179.2 180.0) to 1yh3 #7/B ARG
280  
Applying ASN rotamer (chi angles: 62.2 8.8) to 1yh3 #7/B ASN 290  
Applying PRO rotamer (chi angles: 21.1 -32.4) to 1yh3 #7/B PRO 291  
Applying GLU rotamer (chi angles: -170.4 -83.2 -29.3) to 1yh3 #7/B GLU 292  
Applying ASP rotamer (chi angles: -67.8 -50.2) to 1yh3 #7/B ASP 293  
Applying SER rotamer (chi angles: 68.0) to 1yh3 #7/B SER 294  
Applying SER rotamer (chi angles: 61.0) to 1yh3 #7/B SER 295  
Applying PRO rotamer (chi angles: 27.0 -34.6) to 1b6m.pdb #10/? PRO 1  
Applying PHE rotamer (chi angles: 63.0 90.4) to 1b6m.pdb #10/? PHE 99  
Applying GLN rotamer (chi angles: -171.4 -83.6 145.1) to 1yh3 #11/A GLN 139  
Applying ARG rotamer (chi angles: -178.0 -92.7 178.2 -84.3) to 1yh3 #11/A ARG
247  
Applying GLU rotamer (chi angles: 66.6 -84.1 16.8) to 1yh3 #11/A GLU 248  
Applying ASP rotamer (chi angles: 60.3 -45.5) to 1yh3 #11/A ASP 249  
Applying ARG rotamer (chi angles: 69.0 -77.0 -66.6 163.4) to 1yh3 #11/A ARG
280  
Applying ASN rotamer (chi angles: -63.0 81.5) to 1yh3 #11/A ASN 290  
Applying PRO rotamer (chi angles: -17.2 32.6) to 1yh3 #11/A PRO 291  
Applying GLU rotamer (chi angles: -177.7 65.6 78.7) to 1yh3 #11/A GLU 292  
Applying ASP rotamer (chi angles: -64.0 -9.5) to 1yh3 #11/A ASP 293  
Applying SER rotamer (chi angles: 54.0) to 1yh3 #11/A SER 294  
Applying SER rotamer (chi angles: -65.7) to 1yh3 #11/A SER 295  
Applying GLN rotamer (chi angles: -61.4 -66.0 58.6) to 1yh3 #11/B GLN 139  
Applying ARG rotamer (chi angles: 72.0 -81.7 -164.0 -170.2) to 1yh3 #11/B ARG
140  
Applying ASP rotamer (chi angles: -167.4 1.1) to 1yh3 #11/B ASP 141  
Applying ARG rotamer (chi angles: -84.4 70.3 175.4 175.2) to 1yh3 #11/B ARG
247  
Applying GLU rotamer (chi angles: 66.6 -84.2 17.2) to 1yh3 #11/B GLU 248  
Applying ASP rotamer (chi angles: 62.9 61.0) to 1yh3 #11/B ASP 249  
Applying SER rotamer (chi angles: -64.9) to 1yh3 #11/B SER 250  
Applying ARG rotamer (chi angles: -177.2 177.6 179.2 180.0) to 1yh3 #11/B ARG
280  
Applying ASN rotamer (chi angles: 62.2 8.8) to 1yh3 #11/B ASN 290  
Applying PRO rotamer (chi angles: 21.1 -32.4) to 1yh3 #11/B PRO 291  
Applying GLU rotamer (chi angles: -170.4 -83.2 -29.3) to 1yh3 #11/B GLU 292  
Applying ASP rotamer (chi angles: -67.8 -50.2) to 1yh3 #11/B ASP 293  
Applying SER rotamer (chi angles: 68.0) to 1yh3 #11/B SER 294  
Applying SER rotamer (chi angles: 61.0) to 1yh3 #11/B SER 295  
Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Both O and OXT missing from C-terminal residue 1b6m.pdb #10/? PHE
199; cannot complete teminus  
Not adding hydrogens to 1b6m.pdb #10/? PRO 1 HD2 because it is missing heavy-
atom bond partners  
Not adding hydrogens to 1b6m.pdb #10/? PRO 1 CA because it is missing heavy-
atom bond partners  
Not adding hydrogens to 1b6m.pdb #10/? PRO 1 C because it is missing heavy-
atom bond partners  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
No usable SEQRES records for 1yh3PlacedWaters.pdb (#2) chain A; guessing
termini instead  
No usable SEQRES records for 1yh3PlacedWaters.pdb (#2) chain B; guessing
termini instead  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 1yh3PlacedWaters.pdb
#2/A ARG 45, 1yh3PlacedWaters.pdb #2/B ARG 45  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 1yh3PlacedWaters.pdb #2/A
CYS 296, 1yh3PlacedWaters.pdb #2/B CYS 296  
439 hydrogen bonds  
1yh3PlacedWaters.pdb #2/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3PlacedWaters.pdb #2/B CYS 296 is not terminus, removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Termini for 1yh3 (#7) chain A determined from SEQRES records  
Termini for 1yh3 (#7) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: 1yh3 #7/A ARG 45, 1yh3 #7/B
ARG 45  
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: 1yh3 #7/A CYS 296, 1yh3
#7/B CYS 296  
450 hydrogen bonds  
1yh3 #7/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3 #7/B CYS 296 is not terminus, removing H atom from 'C'  
Termini for 1yh3 (#8) chain A determined from SEQRES records  
Termini for 1yh3 (#8) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: 1yh3 #8/A ARG 45, 1yh3 #8/B
ARG 45  
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: 1yh3 #8/A CYS 296, 1yh3
#8/B CYS 296  
430 hydrogen bonds  
1yh3 #8/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3 #8/B CYS 296 is not terminus, removing H atom from 'C'  
Termini for 1yh3 (#9) chain A determined from SEQRES records  
Termini for 1yh3 (#9) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: 1yh3 #9/A ARG 45, 1yh3 #9/B
ARG 45  
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: 1yh3 #9/A CYS 296, 1yh3
#9/B CYS 296  
430 hydrogen bonds  
1yh3 #9/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3 #9/B CYS 296 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 1b6m.pdb (#10) chain (blank); guessing termini
instead  
Chain-initial residues that are actual N termini: 1b6m.pdb #10/? PRO 1  
Chain-initial residues that are not actual N termini: 1b6m.pdb #10/? PRO 101  
Chain-final residues that are actual C termini: 1b6m.pdb #10/? PHE 199  
Chain-final residues that are not actual C termini: 1b6m.pdb #10/? PHE 99  
162 hydrogen bonds  
Termini for 1yh3 (#11) chain A determined from SEQRES records  
Termini for 1yh3 (#11) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: 1yh3 #11/A ARG 45, 1yh3
#11/B ARG 45  
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: 1yh3 #11/A CYS 296, 1yh3
#11/B CYS 296  
450 hydrogen bonds  
1yh3 #11/A CYS 296 is not terminus, removing H atom from 'C'  
1yh3 #11/B CYS 296 is not terminus, removing H atom from 'C'  
7946 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 142, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 107, in add_standard_charges  
raise ChargeError("Hydrogen %s not bonded to exactly one other atom" % a)  
chimerax.add_charge.charge.ChargeError: Hydrogen 1b6m.pdb #10/? PRO 1 HD2 not
bonded to exactly one other atom  
  
chimerax.add_charge.charge.ChargeError: Hydrogen 1b6m.pdb #10/? PRO 1 HD2 not
bonded to exactly one other atom  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 107, in add_standard_charges  
raise ChargeError("Hydrogen %s not bonded to exactly one other atom" % a)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 450 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro13,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: MBP133.0233.B00
      SMC Version (system): 2.38f7

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 154 days 13:26

Graphics/Displays:

    Intel HD Graphics 530:

      Chipset Model: Intel HD Graphics 530
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x191b
      Revision ID: 0x0006
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 450:

      Chipset Model: AMD Radeon Pro 450
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00ef
      ROM Revision: 113-C980AF-908
      VBIOS Version: 113-C9801AL-028
      EFI Driver Version: 01.00.908
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Bad structure