Opened 5 years ago

Closed 5 years ago

#4006 closed defect (duplicate)

AddH: can't form new hydrogen name

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:        Linux-4.15.0-124-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 266, in _strptime  
month = _months.index(month_name)  
ValueError: tuple.index(x): x not in tuple  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1265, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 38, in nag  
_check_usage(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage  
usage = _get_usage()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 228, in _get_usage  
usage["dates"].append(_strptime(value))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 275, in _strptime  
raise ValueError("time data does not match format")  
ValueError: time data does not match format  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/sasha/Desktop/projects/GPCRmd_str_curation/Antonella_Di_Pizio___Alessandro_Nicoli/6D26/6D26_complex.pdb
> format pdb

Chain information for 6D26_complex.pdb #1  
---  
Chain | Description  
P | No description available  
  

> close session

> open /home/sasha/Desktop/projects/PPI_render/figurec/ACE_SPIKE_complex.pdb
> format pdb

ACE_SPIKE_complex.pdb title:  
The 2019-ncov RBD/ACE2-B0AT1 complex [more info...]  
  
Chain information for ACE_SPIKE_complex.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
X | No description available  
Y Z | No description available  
  
Non-standard residues in ACE_SPIKE_complex.pdb #1  
---  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> set bgColor white

> select /Y:726@CA

2 atoms, 1 residue, 1 model selected  

> select up

8 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

226 atoms, 321 bonds, 16 residues, 1 model selected  

> select up

12206 atoms, 17298 bonds, 749 residues, 1 model selected  

> mlp sel

Map values for surface "ACE_SPIKE_complex.pdb_Y SES surface": minimum -59.56,
mean -8.343, maximum 50.38  

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /Y ARG 768 OXT  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 313, in run  
f(s)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 86, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 171, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/hbond.py", line 213, in add_hydrogens  
_attach_hydrogens(atom, altloc_hpos_info, bonding_info)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/hbond.py", line 893, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 861, in add_altloc_hyds  
pos, bonding_info, alt_loc)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 887, in new_hydrogen  
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 1013, in _h_name  
while find_atom("%s%s" % (h_name, to_h36(h_num, h_digits))):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 952, in to_h36  
decimal_limit = eval('9' * max_digits)  
File "<string>", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 952, in to_h36  
decimal_limit = eval('9' * max_digits)  
  
See log for complete Python traceback.  
  

> select /C:332@CA

1 atom, 1 residue, 1 model selected  

> select /C:1320@N2

1 atom, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> show sel surfaces

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> coulombic sel

Don't know how to assign charges to the following residue types: NAG  

> color bfactor sel

14 atoms, 1 residues, 1 surfaces, atom bfactor range 143 to 143  

> select /C:554@CG

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color bfactor sel

9 atoms, 1 residues, atom bfactor range 135 to 135  

> mlp sel

Map values for surface "ACE_SPIKE_complex.pdb_C SES surface": minimum -28.72,
mean -4.409, maximum 24.88  

> coulombic sel

Atoms with non-standard names found in standard residues: /C SER 469 HXT. Try
deleting all hydrogens first.  

> select /Y:228@N

2 atoms, 1 residue, 1 model selected  

> select up

20 atoms, 30 bonds, 1 residue, 2 models selected  

> select up

150 atoms, 209 bonds, 9 residues, 2 models selected  

> select up

12206 atoms, 17298 bonds, 749 residues, 2 models selected  

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /Y ARG 768 OXT  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 1221, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 376, in try_shortcut  
self.run_shortcut(keys)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 394, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 313, in run  
f(s)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run_expanded_command  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/shortcuts/shortcuts.py", line 480, in run  
run_command(session, command, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/cmd.py", line 97, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/coulombic/coulombic.py", line 86, in assign_charges  
cmd_addh(session, addh_structures, hbond=hbond)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 171, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/hbond.py", line 213, in add_hydrogens  
_attach_hydrogens(atom, altloc_hpos_info, bonding_info)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/hbond.py", line 893, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 861, in add_altloc_hyds  
pos, bonding_info, alt_loc)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 887, in new_hydrogen  
new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema),
"H",  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 1013, in _h_name  
while find_atom("%s%s" % (h_name, to_h36(h_num, h_digits))):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 952, in to_h36  
decimal_limit = eval('9' * max_digits)  
File "<string>", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/addh/cmd.py", line 952, in to_h36  
decimal_limit = eval('9' * max_digits)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 20.0.8
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (WHL GT2)
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: LENOVO
Model: 20N5S01K00
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        4.4G        255M        1.0G         10G        9.7G
	Swap:          2.0G        1.0M        2.0G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3ea0] (rev 02)	
	Subsystem: Lenovo Device [17aa:2279]	
	Kernel driver in use: i915
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
    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
    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: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 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
    distro: 1.5.0
    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 Eric Pettersen, 5 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddH: can't form new hydrogen name

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed

Duplicate of #2717

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