Opened 14 months ago

Closed 14 months ago

#16093 closed defect (can't reproduce)

AddCharge: Hydrogen bonded to atom that should not have hydrogens

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

Description 

The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.8-cp311-cp311-manylinux_2_28_x86_64.whl  

not compatible: wrong platform  

Bundle saved as
/Users/vishnusasi/Downloads/ChimeraX_ISOLDE-1.8-cp311-cp311-manylinux_2_28_x86_64.whl  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Unsupported scale factor (0.000000) detected on Display0  

[Repeated 9 time(s)]

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]

> help help:user

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> open /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7V3P/7V3P.pdb

Chain information for 7V3P.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Dock Prep"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A LYS 897: phi -95.8, psi none trans  
/B LYS 897: phi -125.9, psi none trans  
/A LYS 897 has 2 equal-value rotamers; choosing one arbitrarily.  
Applying LYS rotamer (chi angles: 68.9 76.7 177.2 175.3) to /A LYS 897  
Applying LYS rotamer (chi angles: -62.3 -83.2 88.3 -84.3) to /B LYS 897  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Summary of feedback from adding hydrogens to 7V3P.pdb #1  
---  
notes | No usable SEQRES records for 7V3P.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 7V3P.pdb (#1) chain B; guessing termini instead  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLU 1, /A MET 161, /A
PHE 266, /A PRO 299, /A SER 518, /A CYS 670, /A GLU 744, /B GLU 1, /B ARG 41,
/B CYS 162, /B SER 518, /B CYS 670, /B GLU 744  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 897, /A THR 155, /A
SER 257, /A PRO 293, /A GLN 511, /A LYS 642, /A ARG 704, /B LYS 897, /B ALA
37, /B GLY 154, /B GLN 511, /B LYS 642, /B PRO 705  
877 hydrogen bonds  
Adding 'H' to /A CYS 670  
Adding 'H' to /B CYS 670  
/A LYS 897 is not terminus, removing H atom from 'C'  
/B LYS 897 is not terminus, removing H atom from 'C'  
343 hydrogens added  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7V3P/prepared/7v3p-prep.pdb relModel #1

> close

> open /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7XGD/7xgd.pdb

Chain information for 7xgd.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> ui tool show "Dock Prep"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A LYS 897: phi -141.2, psi none trans  
/B LYS 897: phi -138.5, psi none trans  
Applying LYS rotamer (chi angles: -60.1 -67.0 -174.3 -69.4) to /A LYS 897  
Applying LYS rotamer (chi angles: -60.1 -67.0 -174.3 -69.4) to /B LYS 897  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Summary of feedback from adding hydrogens to 7xgd.pdb #1  
---  
notes | No usable SEQRES records for 7xgd.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 7xgd.pdb (#1) chain B; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1  
Chain-initial residues that are not actual N termini: /A LYS 666, /A GLU 744,
/B LYS 666, /B GLU 744  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 897, /A LYS 642, /A
PRO 705, /B LYS 897, /B LYS 642, /B PRO 705  
927 hydrogen bonds  
Adding 'H' to /A LYS 666  
Adding 'H' to /B LYS 666  
/A LYS 897 is not terminus, removing H atom from 'C'  
/B LYS 897 is not terminus, removing H atom from 'C'  
1070 hydrogens added  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7XGD/prepared/7XGD-prep.pdb relModel #1

> close

> open /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/8TAN/8tan.pdb

Chain information for 8tan.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Dock Prep"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A MET 161: phi -115.8, psi 9.4 trans  
Swapping /A ALA 896 to ALA  
/B MET 161: phi -123.7, psi 45.8 trans  
Swapping /B ALA 896 to ALA  
Applying MET rotamer (chi angles: -64.3 -63.0 -70.3) to /A MET 161  
Applying MET rotamer (chi angles: -65.0 177.4 69.6) to /B MET 161  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Summary of feedback from adding hydrogens to 8tan.pdb #1  
---  
notes | No usable SEQRES records for 8tan.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 8tan.pdb (#1) chain B; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1  
Chain-initial residues that are not actual N termini: /A GLU 264, /A PRO 675,
/A LEU 741, /B GLU 264, /B PRO 297, /B ILE 564, /B LYS 676, /B LEU 741  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 896, /A SER 257, /A
ILE 648, /A PRO 707, /B ALA 896, /B LEU 256, /B CYS 294, /B THR 555, /B ARG
641, /B PRO 707  
1340 hydrogen bonds  
Adding 'H' to /A GLU 264  
Adding 'H' to /A LEU 741  
Adding 'H' to /B GLU 264  
Adding 'H' to /B ILE 564  
Adding 'H' to /B LYS 676  
1 messages similar to the above omitted  
/A ALA 896 is not terminus, removing H atom from 'C'  
/B ALA 896 is not terminus, removing H atom from 'C'  
12894 hydrogens added  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/8TAN/prepared/8TAN-prep.pdb relModel #1

> close

> open /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-work/LightDock/QP-
> apo/IGFR_apo.pdb

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

> ui tool show "Dock Prep"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Summary of feedback from adding hydrogens to IGFR_apo.pdb #1  
---  
notes | No usable SEQRES records for IGFR_apo.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for IGFR_apo.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 902, /B ASN 902  
Chain-final residues that are not actual C termini:  
1410 hydrogen bonds  
74 hydrogens added  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-work/LightDock/QP-apo/QP-
> apo-prep.pdb relModel #1

> close

> open /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-work/LightDock/7XGD/7XGD-
> chainA.pdb

Chain information for 7XGD-chainA.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Dock Prep"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A LYS 897: phi -141.2, psi none trans  
Applying LYS rotamer (chi angles: -60.1 -67.0 -174.3 -69.4) to /A LYS 897  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Summary of feedback from adding hydrogens to 7XGD-chainA.pdb #1  
---  
notes | No usable SEQRES records for 7XGD-chainA.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 1  
Chain-initial residues that are not actual N termini: /A LYS 666, /A GLU 744  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 897, /A LYS 642, /A
PRO 705  
457 hydrogen bonds  
Adding 'H' to /A LYS 666  
/A LYS 897 is not terminus, removing H atom from 'C'  
558 hydrogens added  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7XGD/prepared/7XGD-chainAprep.pdb relModel #1

> open /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7XGD/prepared/7xgd-chainA-fast-modeller-prep.pdb

Chain information for 7xgd-chainA-fast-modeller-prep.pdb  
---  
Chain | Description  
2.1/A | No description available  
2.2/A | No description available  
  

> select : 643-669

485 atoms, 487 bonds, 35 residues, 3 models selected  

> select : 706-743

597 atoms, 598 bonds, 38 residues, 1 model selected  

> select : 706-744

642 atoms, 641 bonds, 41 residues, 3 models selected  

> select : 643-669, 706-743

1082 atoms, 1085 bonds, 73 residues, 3 models selected  

> select : 643-669, 706-744

1127 atoms, 1128 bonds, 76 residues, 3 models selected  

> hide #!1 models

> hide #!2.1 models

> select : 643-669, 706-745

1190 atoms, 1194 bonds, 79 residues, 3 models selected  

> select : 643-669, 706-746

1232 atoms, 1239 bonds, 82 residues, 3 models selected  

> select : 643-669, 706-743\

1082 atoms, 1085 bonds, 73 residues, 3 models selected  

> select : 643-669, 706-743

1082 atoms, 1085 bonds, 73 residues, 3 models selected  

> close

> open 3i40 fromDatabase pdb format mmcif

3i40 title:  
Human insulin [more info...]  
  
Chain information for 3i40 #1  
---  
Chain | Description | UniProt  
A | Insulin A chain | INS_HUMAN 1-21  
B | Insulin B chain | INS_HUMAN 1-30  
  
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show "Dock Prep"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Summary of feedback from adding hydrogens to 3i40 #1  
---  
notes | Termini for 3i40 (#1) chain A determined from SEQRES records  
Termini for 3i40 (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLY 1, /B PHE 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASN 21, /B ALA 30  
Chain-final residues that are not actual C termini:  
35 hydrogen bonds  
379 hydrogens added  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7V3P/insulin_prep_untransformed_coordinates.pdb relModel #1

> save /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7V3P/insulin_prep_transformed_coordinates.pdb

> close

> open /Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
> work/LightDock/7V3P/prepared/lightdock_49.pdb

Summary of feedback from opening
/Users/vishnusasi/Documents/Vishnu_Work/9-Oct-
work/LightDock/7V3P/prepared/lightdock_49.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 16  
200 messages similar to the above omitted  
  
Chain information for lightdock_49.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Dock Prep"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A ASN 21: phi -160.2, psi none trans  
Swapping /B ALA 30 to ALA  
Applying ASN rotamer (chi angles: -70.4 -23.2) to /A ASN 21  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Summary of feedback from adding hydrogens to lightdock_49.pdb #1  
---  
notes | No usable SEQRES records for lightdock_49.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for lightdock_49.pdb (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1  
Chain-initial residues that are not actual N termini: /A MET 161, /A PHE 266,
/A PRO 299, /A SER 518, /A CYS 670, /A GLU 744, /B ARG 41, /B CYS 162, /B SER
518, /B CYS 670, /B GLU 744  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 21, /A THR 155, /A
SER 257, /A PRO 293, /A GLN 511, /A LYS 642, /A ARG 704, /B ALA 30, /B ALA 37,
/B GLY 154, /B GLN 511, /B LYS 642, /B PRO 705  
1057 hydrogen bonds  
Adding 'H' to /A MET 161  
Adding 'H' to /A PHE 266  
Adding 'H' to /A SER 518  
Adding 'H' to /A CYS 670  
Adding 'H' to /A GLU 744  
5 messages similar to the above omitted  
/A ASN 21 is not terminus, removing H atom from 'C'  
/B ALA 30 is not terminus, removing H atom from 'C'  
13158 hydrogens added  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 129, in add_standard_charges  
h.charge, h.gaff_type = hyd_charge_type_data[(h.residue.amber_name,
heavy.name.lower())]  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
KeyError: ('LYS', 'c')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 146, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 131, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
chimerax.add_charge.charge.ChargeError: Hydrogen /A LYS 897 H bonded to atom
that should not have hydrogens (/A LYS 897 C)  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A LYS 897 H bonded to atom
that should not have hydrogens (/A LYS 897 C)  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 131, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
  
See log for complete Python traceback.  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 580.140.1~8

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 2 days, 6 hours, 3 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        24V2W1G5:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Adapter Firmware Version: 15.90
        DELL SE2219H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: JRJGQZ2     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Adapter Firmware Version: 15.90


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 14 months ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddCharge: Hydrogen bonded to atom that should not have hydrogens

comment:2 by Eric Pettersen, 14 months ago

Resolution: → can't reproduce
Status: accepted → closed

Would need the structure to see how this happened.

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