OpenMM 7.6

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
The OpenMM team have announced their 7.6 release candidate, and all going well expect to do the official release next week. Would be good to get it into ChimeraX for 1.3. From their discussion at https://github.com/openmm/openmm/issues/3191, it looks like they're planning on officially supporting PyPI builds for the next release, so this should hopefully be the last time that this custom bundling into ChimeraX approach will be required.

As an aside: do you have a timeframe for 1.3? I'm hoping it's not *too* soon - there are a few AlphaFold-related things I'd like to get polished in ISOLDE before the next release, but I've been absolutely buried in conferences, workshops, manuscript revisions, etc. etc.. Hopefully some clear coding space to come soon!

OpenGL version: 3.3.0 NVIDIA 471.11
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB
Locale: ('en_GB', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Tom Goddard]

How about we wait for the official 7.6 OpenMM release then we can put it in the daily builds?

We just discussed the ChimeraX 1.3 release schedule at yesterday's group meeting, aiming for a release candidate in about a month, the second half of September. I put the schedule on the 1.3 Roadmap web page, ​https://www.rbvi.ucsf.edu/trac/ChimeraX/milestone/1.3

Approximate Schedule
September 15 - October 1, 2021: First release candidate
October 2021: Fixing bugs in release candidates, until 2 weeks with no new fixes.
Oct 31, 2021: Production release.

I have an alphafold command in ChimeraX that can do fetching, sequence searching with blat or blast, and prediction from sequence using Google Colab. It is all in a somewhat rough state, but plan to get it working well for the 1.3 release. Also giving a webinar on it at a Stanford cryoEM workshop Sept 8-10 that I think you are presenting at too.

[Tristan Croll]

Yep - waiting for the 7.6 release sounds good to me. Just wanted to make sure it's on the radar. Timeframe for ChimeraX 1.3 sounds good.

I'm working on making ISOLDE's reference-model distance and torsion restraints adjust themselves at the per-restraint level based on the PAE matrix and pLDDT values - basically to make restraints to lower-confidence sites both weaker and fuzzier. Looking promising, but a fair bit more work to do (would also like to add in a non-command-based interface, but still have to work out what that would look like).
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 20 August 2021 19:06
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5084: OpenMM 7.6

#5084: OpenMM 7.6
------------------------------------+-------------------------
          Reporter:  Tristan Croll  |      Owner:  Tom Goddard
              Type:  task           |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Third Party    |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------

Comment (by Tom Goddard):

 How about we wait for the official 7.6 OpenMM release then we can put it
 in the daily builds?

 We just discussed the ChimeraX 1.3 release schedule at yesterday's group
 meeting, aiming for a release candidate in about a month, the second half
 of September.  I put the schedule on the 1.3 Roadmap web page,
 https://www.rbvi.ucsf.edu/trac/ChimeraX/milestone/1.3

 Approximate Schedule
 September 15 - October 1, 2021: First release candidate
 October 2021: Fixing bugs in release candidates, until 2 weeks with no new
 fixes.
 Oct 31, 2021: Production release.

 I have an alphafold command in ChimeraX that can do fetching, sequence
 searching with blat or blast, and prediction from sequence using Google
 Colab.  It is all in a somewhat rough state, but plan to get it working
 well for the 1.3 release.  Also giving a webinar on it at a Stanford
 cryoEM workshop Sept 8-10 that I think you are presenting at too.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5084#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tristan Croll]

OpenMM 7.6.0 is released. A few teething issues (https://github.com/openmm/openmm/issues/3232), but nothing that should badly affect ChimeraX or ISOLDE. Linux devtoolset-9/CUDA 11.2 build is attached; as usual the MacOS and Windows builds should be fine to use from Conda. Is there any chance of slotting this into the daily builds before Thursday? It would be great to be able to use it for the Stanford cryo-EM meeting.

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 20 August 2021 19:27
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5084: OpenMM 7.6

#5084: OpenMM 7.6
------------------------------------+-------------------------
          Reporter:  Tristan Croll  |      Owner:  Tom Goddard
              Type:  task           |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Third Party    |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------

Comment (by Tristan Croll):

 {{{
 Yep - waiting for the 7.6 release sounds good to me. Just wanted to make
 sure it's on the radar. Timeframe for ChimeraX 1.3 sounds good.

 I'm working on making ISOLDE's reference-model distance and torsion
 restraints adjust themselves at the per-restraint level based on the PAE
 matrix and pLDDT values - basically to make restraints to lower-confidence
 sites both weaker and fuzzier. Looking promising, but a fair bit more work
 to do (would also like to add in a non-command-based interface, but still
 have to work out what that would look like).
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: 20 August 2021 19:06
 Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll
 <tic20@cam.ac.uk>
 Subject: Re: [ChimeraX] #5084: OpenMM 7.6

 #5084: OpenMM 7.6
 ------------------------------------+-------------------------
           Reporter:  Tristan Croll  |      Owner:  Tom Goddard
               Type:  task           |     Status:  assigned
           Priority:  normal         |  Milestone:
          Component:  Third Party    |    Version:
         Resolution:                 |   Keywords:
         Blocked By:                 |   Blocking:
 Notify when closed:                 |   Platform:  all
            Project:  ChimeraX       |
 ------------------------------------+-------------------------

 Comment (by Tom Goddard):

  How about we wait for the official 7.6 OpenMM release then we can put it
  in the daily builds?

  We just discussed the ChimeraX 1.3 release schedule at yesterday's group
  meeting, aiming for a release candidate in about a month, the second half
  of September.  I put the schedule on the 1.3 Roadmap web page,
  https://www.rbvi.ucsf.edu/trac/ChimeraX/milestone/1.3

  Approximate Schedule
  September 15 - October 1, 2021: First release candidate
  October 2021: Fixing bugs in release candidates, until 2 weeks with no
 new
  fixes.
  Oct 31, 2021: Production release.

  I have an alphafold command in ChimeraX that can do fetching, sequence
  searching with blat or blast, and prediction from sequence using Google
  Colab.  It is all in a somewhat rough state, but plan to get it working
  well for the 1.3 release.  Also giving a webinar on it at a Stanford
  cryoEM workshop Sept 8-10 that I think you are presenting at too.

 --
 Ticket URL:
 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5084#comment:2>
 ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
 ChimeraX Issue Tracker
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5084#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

openmm-7.6.0-linux-py39_cuda112_1.tar.bz2​

[Tristan Croll]

Added by email2trac

[goddard@…]

It seems a bit reckless to update OpenMM two days before your workshop presentation.  I could possibly do that, but I have a presentation to give at the same workshop tomorrow morning, and doing the update will require me to install and test on all platforms (Windows, Linux and Mac) and I don't know if I will have time for that today since I am preparing my talk.  How badly do you want this?

[Tristan Croll]

Well, I can do the demo in the ChimeraX 1.2 /ISOLDE 1.2 release version, but it would be nice to be able to show off the new AlphaFold features. On my Linux machine I've been using the OpenMM PyPI build I made a few months ago, which was already using the OpenMM 7.6-style imports ("from simtk.openmm import..." replaced with "from openmm import...". Seemed sensible at the time, but it now means that I can't work with the ChimeraX daily build in other platforms until OpenMM is updated. But it's far from critical... after my talk I'll only have about 20 min for a quick demo anyway.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 07 September 2021 20:20
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5084: OpenMM 7.6

#5084: OpenMM 7.6
------------------------------------+-------------------------
          Reporter:  Tristan Croll  |      Owner:  Tom Goddard
              Type:  task           |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Third Party    |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------

Comment (by goddard@…):

 {{{
 It seems a bit reckless to update OpenMM two days before your workshop
 presentation.  I could possibly do that, but I have a presentation to give
 at the same workshop tomorrow morning, and doing the update will require
 me to install and test on all platforms (Windows, Linux and Mac) and I
 don't know if I will have time for that today since I am preparing my
 talk.  How badly do you want this?
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5084#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

Ok I updated OpenMM to 7.6.0 in ChimeraX using your Linux tar ball and the Mac and Windows binaries from conda-forge. I only install site-packages/openmm not site-packages/simtk since I believe the simtk module is deprecated. I tested the tug/minimize mouse modes on Mac, Windows and Linux, all working. I have not tested ISOLDE.

We probably should have updated to 7.6.0 a while ago since we plan on releasing ChimeraX 1.3 in October. But given you have been using it since July, putting it in now should still give us enough time to see it is working well before release.