Opened 5 years ago

Closed 3 years ago

#4018 closed defect (fixed)

ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds between residues

Reported by: kartik.manne@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
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/kartikmanne/Documents/DH898.1/DH898.1_apotrimer/DH898p1_fitModel_P67_J2290_apoTrimer-1_real_space_refined_RR11.pdb

Chain information for
DH898p1_fitModel_P67_J2290_apoTrimer-1_real_space_refined_RR11.pdb #1  
---  
Chain | Description  
a c e | No description available  
b d f | No description available  
  

> set bgColor white

> open
> /home/kartikmanne/Documents/DH898.1/DH898.1_apotrimer/cryosparc_P67_J229__localfilter.mrc

Opened cryosparc_P67_J229__localfilter.mrc, grid size 256,256,256, pixel 1.07,
shown at level 0.313, step 1, values float32  

> clipper associate #2 toModel #1

Chain information for
DH898p1_fitModel_P67_J2290_apoTrimer-1_real_space_refined_RR11.pdb  
---  
Chain | Description  
1.2/a 1.2/c 1.2/e | No description available  
1.2/b 1.2/d 1.2/f | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> clipper spotlight radius 32.00

> clipper spotlight radius 32.00

> select #1

29361 atoms, 29835 bonds, 6 pseudobonds, 1929 residues, 13 models selected  
Traceback (most recent call last):  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2727, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 616, in __init__  
raise e  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 595, in __init__  
isolde.forcefield_mgr)  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
template_dict = find_residue_templates(sim_construct.all_residues, ff,
ligand_db=ligand_db, logger=session.logger)  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3105, in
find_residue_templates  
tname, prot_res = find_glycan_template_name_and_link(sugar)  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 250, in
find_glycan_template_name_and_link  
r.chain_id, r.number, n.chain_id, n.number  
RuntimeError: Residue a515 has multiple bonds to neighbor a516  
  
RuntimeError: Residue a515 has multiple bonds to neighbor a516  
  
File "/home/kartikmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 250, in
find_glycan_template_name_and_link  
r.chain_id, r.number, n.chain_id, n.number  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 430.40
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: TYAN
Model: B7105F48TV8HR-2T-G
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           187G        6.6G        175G        170M        5.5G        179G
	Swap:            9G          0B          9G

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]	
	Kernel driver in use: ast
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    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
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    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
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    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
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    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
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    ChimeraX-ColorGlobe: 1.0
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    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-ISOLDE: 1.1.0
    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
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    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
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    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-Phenix: 0.1
    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
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    Pillow: 7.1.2
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
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    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
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    tinyarray: 1.2.2
    tornado: 6.0.4
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    urllib3: 1.25.10
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Change History (7)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds between residues

comment:2 by Tristan Croll, 5 years ago

The problem here is that you have something wrong with the bonding between sugar residues a515 and a516 - there are (at least) two bonds between them, which is almost certainly not what you want. I'll tweak the code so cases like this bring up a more informative dialogue and focus the view on the offending site, but for now you'll want to take a close look to see what's wrong. Note that the ISOLDE menu has a few simple tools included that can help with the editing necessary to fix this (add/remove bond, add hydrogen).

in reply to:  3 ; comment:3 by kartik.manne@…, 5 years ago 

Hi,

I'm also getting this error and the program crashes. Do you know what it means?

Gtk-Message: 12:37:22.116: GtkDialog mapped without a transient parent. This is discouraged.
Fatal Python error: Segmentation fault

Thread 0x00007fa4427fd700 (most recent call first):
  File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 300 in wait
  File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 552 in wait
  File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 1175 in run
  File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 926 in _bootstrap_inner
  File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 890 in _bootstrap

Current thread 0x00007fa4effd1740 (most recent call first):
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py", line 93 in get_prop
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/addh/hbond.py", line 84 in add_hydrogens
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/addh/cmd.py", line 171 in hbond_add_hydrogens
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/addh/cmd.py", line 63 in cmd_addh
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805 in run
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 275 in execute
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 112 in keyPressEvent
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line 269 in event_loop
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py", line 772 in init
  File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py", line 919 in <module>
  File "/opt/UCSF/ChimeraX/lib/python3.7/runpy.py", line 85 in _run_code
  File "/opt/UCSF/ChimeraX/lib/python3.7/runpy.py", line 193 in _run_module_as_main
Segmentation fault

Thanks,
Kartik
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, December 4, 2020 12:05 PM
Cc: Kartik Manne, Ph.D. <kartik.manne@duke.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4018: ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds between residues (was: ChimeraX bug report submission)

#4018: ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds between
residues
-------------------------------------+---------------------------
          Reporter:  kartik.manne@…  |      Owner:  Tristan Croll
              Type:  defect          |     Status:  assigned
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+---------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tristan Croll


--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4018*comment:1__;Iw!!OToaGQ!_y_msPoJrxNnn4olpqFsUZJlc-3z9sNW6VzxHCDZlMygfJdVIpZKmDZDjt4q621Lk2o$ >
ChimeraX <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimerax/__;!!OToaGQ!_y_msPoJrxNnn4olpqFsUZJlc-3z9sNW6VzxHCDZlMygfJdVIpZKmDZDjt4q2MTlVZA$ >
ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added

I believe that issue was fixed on 10/19, so the fix is only in the 1.2 daily build unfortunately. I'll try to get an updated AddH bundle onto the toolshed today. Will alert you once it's available.

--Eric

in reply to:  5 ; comment:5 by Tristan Croll, 5 years ago 

(Sorry for the duplicate - replied directly to you rather than to the bug tracker).

That looks like a bug in AddH that's fixed in the daily builds (for which I unfortunately don't have an ISOLDE version yet). To avoid it, I'm afraid you'll need to delete the existing hydrogens before running AddH again ("del H; addh").
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 04 December 2020 17:41
To: kartik.manne@duke.edu <kartik.manne@duke.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4018: ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds between residues

#4018: ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds between
residues
-------------------------------------+---------------------------
          Reporter:  kartik.manne@…  |      Owner:  Tristan Croll
              Type:  defect          |     Status:  assigned
          Priority:  normal          |  Milestone:
         Component:  Third Party     |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+---------------------------

Comment (by kartik.manne@…):

 {{{
 Hi,

 I'm also getting this error and the program crashes. Do you know what it
 means?

 Gtk-Message: 12:37:22.116: GtkDialog mapped without a transient parent.
 This is discouraged.
 Fatal Python error: Segmentation fault

 Thread 0x00007fa4427fd700 (most recent call first):
   File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 300 in wait
   File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 552 in wait
   File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 1175 in run
   File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 926 in
 _bootstrap_inner
   File "/opt/UCSF/ChimeraX/lib/python3.7/threading.py", line 890 in
 _bootstrap

 Current thread 0x00007fa4effd1740 (most recent call first):
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/atomic/molc.py", line 93 in get_prop
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/addh/hbond.py", line 84 in add_hydrogens
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/addh/cmd.py", line 171 in hbond_add_hydrogens
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/addh/cmd.py", line 63 in cmd_addh
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/core/commands/cli.py", line 2805 in run
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/cmd_line/tool.py", line 275 in execute
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/cmd_line/tool.py", line 112 in keyPressEvent
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/ui/gui.py", line 269 in event_loop
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py",
 line 772 in init
   File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ChimeraX_main.py",
 line 919 in <module>
   File "/opt/UCSF/ChimeraX/lib/python3.7/runpy.py", line 85 in _run_code
   File "/opt/UCSF/ChimeraX/lib/python3.7/runpy.py", line 193 in
 _run_module_as_main
 Segmentation fault

 Thanks,
 Kartik
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: Friday, December 4, 2020 12:05 PM
 Cc: Kartik Manne, Ph.D. <kartik.manne@duke.edu>; tic20@cam.ac.uk
 <tic20@cam.ac.uk>
 Subject: Re: [ChimeraX] #4018: ISOLDE: OpenMM:
 find_glycan_template_name_and_link: multiple bonds between residues (was:
 ChimeraX bug report submission)

 #4018: ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds
 between
 residues
 -------------------------------------+---------------------------
           Reporter:  kartik.manne@…  |      Owner:  Tristan Croll
               Type:  defect          |     Status:  assigned
           Priority:  normal          |  Milestone:
          Component:  Third Party     |    Version:
         Resolution:                  |   Keywords:
         Blocked By:                  |   Blocking:
 Notify when closed:                  |   Platform:  all
            Project:  ChimeraX        |
 -------------------------------------+---------------------------
 Changes (by Eric Pettersen):

  * status:  new => assigned
  * component:  Unassigned => Third Party
  * project:   => ChimeraX
  * platform:   => all
  * owner:  (none) => Tristan Croll


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Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4018#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:6 by Eric Pettersen, 5 years ago

Okay, I have uploaded an AddH bundle to the Toolshed that contains the fix. You should be able to install it via the Tools→More Tools... menu item.

--Eric

comment:7 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed
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