Opened 5 years ago

Closed 5 years ago

#4315 closed defect (not a bug)

Coulombic failure due to unexpected hydrogen name

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

Description 

The following bug report has been submitted:
Platform:        Darwin-20.3.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Trying to view structure with electrostatic colouring and it reported a keyerror of 'HXT' 

Thanks for any help!

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_AddH-2.1.3-py3-none-any.whl  
Traceback (most recent call last):  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 389, in download_finished  
session=self.session)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  

> open 6nwv format mmcif fromDatabase pdb

Summary of feedback from opening 6nwv fetched from pdb  
---  
warnings | Atom OE1 has no neighbors to form bonds with according to residue
template for GLU /C:4  
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /C:4  
Atom CE2 has no neighbors to form bonds with according to residue template for
PHE /F:1  
Atom N has no neighbors to form bonds with according to residue template for
THR /F:30  
Atom OXT has no neighbors to form bonds with according to residue template for
THR /F:30  
Atom N has no neighbors to form bonds with according to residue template for
THR /L:30  
Atom OXT has no neighbors to form bonds with according to residue template for
THR /L:30  
  
6nwv title:  
Insulin Lispro Analog [more info...]  
  
Chain information for 6nwv #1  
---  
Chain | Description  
A C E G I K | Insulin A chain  
B D F H J L | Insulin Lispro B chain  
  
Non-standard residues in 6nwv #1  
---  
CL — chloride ion  
CRS — M-cresol  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
ZN — zinc ion  
  

> mlp

Map values for surface "6nwv_A SES surface": minimum -26.76, mean -3.309,
maximum 21.28  
Map values for surface "6nwv_B SES surface": minimum -23.39, mean -1.341,
maximum 22.07  
Map values for surface "6nwv_C SES surface": minimum -28.39, mean -5.06,
maximum 20.01  
Map values for surface "6nwv_D SES surface": minimum -21.98, mean -1.476,
maximum 21.46  
Map values for surface "6nwv_E SES surface": minimum -27.15, mean -4.3,
maximum 19.64  
Map values for surface "6nwv_F SES surface": minimum -22.1, mean -1.424,
maximum 22.05  
Map values for surface "6nwv_G SES surface": minimum -23.02, mean -3.498,
maximum 20.32  
Map values for surface "6nwv_H SES surface": minimum -22.46, mean -1.286,
maximum 22.31  
Map values for surface "6nwv_I SES surface": minimum -25.09, mean -3.88,
maximum 20.31  
Map values for surface "6nwv_J SES surface": minimum -22.21, mean -1.501,
maximum 21.4  
Map values for surface "6nwv_K SES surface": minimum -25.48, mean -3.247,
maximum 19.19  
Map values for surface "6nwv_L SES surface": minimum -23.08, mean -1.273,
maximum 22.21  

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /L GLU 21 OE1, /H PRO 29 CG, /H PRO 29 CB, /H PRO
29 CD, /H THR 30 C, and 78 other atoms  

/F THR 30 HXT  
Traceback (most recent call last):  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 313, in run  
f(s)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 96, in assign_charges  
assign_residue_charges(charged_residues, his_scheme)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
KeyError: 'HXT'  
  
KeyError: 'HXT'  
  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
  
See log for complete Python traceback.  
  

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /L GLU 21 OE1, /H PRO 29 CG, /H PRO 29 CB, /H PRO
29 CD, /H THR 30 C, and 78 other atoms  

/F THR 30 HXT  
Traceback (most recent call last):  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 202, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1273, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 313, in run  
f(s)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 96, in assign_charges  
assign_residue_charges(charged_residues, his_scheme)  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
KeyError: 'HXT'  
  
KeyError: 'HXT'  
  
File
"/private/var/folders/8q/lthrg_fs34jfd_vsbxhxqhpm0000gn/T/AppTranslocation/526C5BF1-8743-4868-8EC0-C250199FF142/d/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 161, in assign_residue_charges  
a.charge = res_data[aname]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.1.11
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro13,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.9 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 429.80.1.0.0
      SMC Version (system): 2.37f25

Software:

    System Software Overview:

      System Version: macOS 11.2.1 (20D74)
      Kernel Version: Darwin 20.3.0
      Time since boot: 15 days 6:31

Graphics/Displays:

    Intel Iris Graphics 550:

      Chipset Model: Intel Iris Graphics 550
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1927
      Revision ID: 0x000a
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2419H:
          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: BC01V13     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Coulombic failure due to unexpected hydrogen name

comment:2 by pett, 5 years ago

Resolution: → not a bug
Status: accepted → closed

Hi Gus,

In order for coulombic to add hydrogens and assign accurate charges, residues need to have all their heavy atoms. 6nwv has many residues missing heavy atoms, some of them backbone atoms. This prevents ChimeraX from adding hydrogens correctly. Deleting a few of these with the command "del /D,F,L:30" allows coulombic to run, but as per it's output in the log, many other residues are still incomplete, so you should take any electrostatic rendering it creates with a fairly large grain of salt.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Note: See TracTickets for help on using tickets.