Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#4037 closed defect (fixed)

Could not find a version that satisfies the requirement ChimeraX-AddH==2.1.3

Reported by: weberm@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
I started ChimeraX today and was prompted with an option to update which I did, but: the update did not work automatically. Instead I got the following message. I think this should all work automatically to make things more convenient to non IT specialist users.

Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ 
ERROR: Could not find a version that satisfies the requirement ChimeraX-AddH==2.1.3 
ERROR: No matching distribution found for ChimeraX-AddH==2.1.3 
WARNING: You are using pip version 20.2.2; however, version 20.3.1 is available. 
You should consider upgrading via the 'C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe -m pip install --upgrade pip' command. 

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\weber\\\Desktop\\\Alien-13\\\Silvestrol\\\SwissDock\\\movie_MW_1_RNA.cxs

Log from Sun Aug 30 20:29:57 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/weber/Desktop/Alien-13/Silvestrol/5zc9.cif

5zc9.cif title:  
Crystal structure of the human eIF4A1-ATP analog-RocA-polypurine RNA complex
[more info...]  
  
Chain information for 5zc9.cif #1  
---  
Chain | Description  
A | Eukaryotic initiation factor 4A-I  
B | RNA (5'-R(*ap*GP*ap*GP*ap*GP*ap*GP*ap*G)-3')  
  
Non-standard residues in 5zc9.cif #1  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
RCG —
(1R,2R,3S,3aR,8bS)-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-1,8b-bis(oxidanyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxamide
(Rocaglamide, Rocaglamide A)  
  

> open
> C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/MW_1_swissdockd_AeK_pL_3E5OAM1994OBEFGOYIJS/clusters.dock4.pdb

Summary of feedback from opening
C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/MW_1_swissdockd_AeK_pL_3E5OAM1994OBEFGOYIJS/clusters.dock4.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Energy: 79.7604  
  
Ignored bad PDB record found on line 2  
REMARK SimpleFitness: 79.7604  
  
Ignored bad PDB record found on line 3  
REMARK FullFitness: -2096.6875  
  
Ignored bad PDB record found on line 4  
REMARK InterFull: -48.9961  
  
Ignored bad PDB record found on line 5  
REMARK IntraFull: 95.6238  
  
33 messages similar to the above omitted  
Duplicate atom serial number found: 6838  
Duplicate atom serial number found: 6839  
Duplicate atom serial number found: 6840  
Duplicate atom serial number found: 6841  
Duplicate atom serial number found: 6842  
63 messages similar to the above omitted  
Ignored bad PDB record found on line 177  
REMARK Energy: 79.9944  
  
Ignored bad PDB record found on line 178  
REMARK SimpleFitness: 79.9944  
  
Ignored bad PDB record found on line 179  
REMARK FullFitness: -2096.238  
  
Ignored bad PDB record found on line 180  
REMARK InterFull: -48.3594  
  
Ignored bad PDB record found on line 181  
REMARK IntraFull: 95.6265  
  
[deleted many messages like these]

Ignored bad PDB record found on line 22443  
REMARK FullFitness: -2058.419  
  
Ignored bad PDB record found on line 22444  
REMARK InterFull: -27.1339  
  
Ignored bad PDB record found on line 22445  
REMARK IntraFull: 115.211  
  
14 messages similar to the above omitted  
Duplicate atom serial number found: 6838  
Duplicate atom serial number found: 6839  
Duplicate atom serial number found: 6840  
Duplicate atom serial number found: 6841  
Duplicate atom serial number found: 6842  
63 messages similar to the above omitted  
  

> close session

> open
> C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/MW_1_swissdockd_AeK_pL_3E5OAM1994OBEFGOYIJS/target.pdb

Summary of feedback from opening
C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/MW_1_swissdockd_AeK_pL_3E5OAM1994OBEFGOYIJS/target.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK PYCHARMM CRD  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 8/30/20 18:43:57 CREATED BY USER: root  
  
Chain information for target.pdb #1  
---  
Chain | Description  
| No description available  
  

> open
> C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/MW_1_swissdockd_AeK_pL_3E5OAM1994OBEFGOYIJS/clusters.dock4.pdb

Summary of feedback from opening
C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/MW_1_swissdockd_AeK_pL_3E5OAM1994OBEFGOYIJS/clusters.dock4.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Energy: 79.7604  
  
Ignored bad PDB record found on line 2  
REMARK SimpleFitness: 79.7604  
  
Ignored bad PDB record found on line 3  
REMARK FullFitness: -2096.6875  
  
Ignored bad PDB record found on line 4  
REMARK InterFull: -48.9961  
  
Ignored bad PDB record found on line 5  
REMARK IntraFull: 95.6238  
  
33 messages similar to the above omitted  
Duplicate atom serial number found: 6838  
Duplicate atom serial number found: 6839  
Duplicate atom serial number found: 6840  
Duplicate atom serial number found: 6841  
Duplicate atom serial number found: 6842  
63 messages similar to the above omitted  
Ignored bad PDB record found on line 177  
REMARK Energy: 79.9944  
  
Ignored bad PDB record found on line 178  
REMARK SimpleFitness: 79.9944  
  
Ignored bad PDB record found on line 179  
REMARK FullFitness: -2096.238  
  
Ignored bad PDB record found on line 180  
REMARK InterFull: -48.3594  
  
Ignored bad PDB record found on line 181  
REMARK IntraFull: 95.6265  
  
14 messages similar to the above omitted  
Duplicate atom serial number found: 6838  
Duplicate atom serial number found: 6839  
Duplicate atom serial number found: 6840  
Duplicate atom serial number found: 6841  
Duplicate atom serial number found: 6842  
63 messages similar to the above omitted  
Ignored bad PDB record found on line 265  
REMARK Energy: 81.0083  
  

[deleted many messages like these]
  
Ignored bad PDB record found on line 22357  
REMARK IntraFull: 115.458  
  
14 messages similar to the above omitted  
Duplicate atom serial number found: 6838  
Duplicate atom serial number found: 6839  
Duplicate atom serial number found: 6840  
Duplicate atom serial number found: 6841  
Duplicate atom serial number found: 6842  
63 messages similar to the above omitted  
Ignored bad PDB record found on line 22441  
REMARK Energy: 109.88  
  
Ignored bad PDB record found on line 22442  
REMARK SimpleFitness: 109.88  
  
Ignored bad PDB record found on line 22443  
REMARK FullFitness: -2058.419  
  
Ignored bad PDB record found on line 22444  
REMARK InterFull: -27.1339  
  
Ignored bad PDB record found on line 22445  
REMARK IntraFull: 115.211  
  
14 messages similar to the above omitted  
Duplicate atom serial number found: 6838  
Duplicate atom serial number found: 6839  
Duplicate atom serial number found: 6840  
Duplicate atom serial number found: 6841  
Duplicate atom serial number found: 6842  
63 messages similar to the above omitted  
  

> show surfaces

> undo

> hide surfaces

> open C:/Users/weber/Desktop/Alien-13/Silvestrol/5zc9.pdb

5zc9.pdb title:  
Crystal structure of the human EIF4A1-atp analog-roca-polypurine RNA complex
[more info...]  
  
Chain information for 5zc9.pdb #3  
---  
Chain | Description  
A | eukaryotic initiation factor 4A-I  
B | RNA (5'-R(*ap*GP*ap*GP*ap*GP*ap*GP*ap*G)-3')  
  
Non-standard residues in 5zc9.pdb #3  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
RCG —
(1R,2R,3S,3AR,8BS)-6,8-dimethoxy-3A-(4-methoxyphenyl)-N,N-dimethyl-1,8B-bis(oxidanyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[B][1]benzofuran-2-carboxamide
(rocaglamide, rocaglamide A)  
  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker target.pdb, chain (blank) (#1) with 5zc9.pdb, chain A (#3),
sequence alignment score = 1889.6  
RMSD between 378 pruned atom pairs is 0.038 angstroms; (across all 378 pairs:
0.038)  
  

> hide #2 models

> turn y 180

> turn y -180

> turn y 90

> turn y -90

> turn y 120

> show #2 models

> hide #2 models

> show #2 models

> save C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/MW-1.cxs

> select ::name="RCG"

37 atoms, 41 bonds, 1 model selected  

> hide #2 models

> show #2 models

> select clear

> select nucleic-acid

222 atoms, 251 bonds, 1 model selected  

> lighting full

> show sel surfaces

> color (#!3 & sel) lime

> hide #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #1

6837 atoms, 6634 bonds, 1 model selected  

> show sel surfaces

> hide #!3 models

> show #!3 models

> hide #!3 models

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> show #!1 models

> show #!3 models

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\weber\Desktop\movie1.mp4

Movie saved to \C:Users\\...\Desktop\movie1.mp4  
  

> hide #!3 models

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\weber\Desktop\movie2.mp4

Movie saved to \C:Users\\...\Desktop\movie2.mp4  
  

> show #!3 models

> save C:/Users/weber/Desktop/Alien-13/Silvestrol/SwissDock/movie_MW_1_RNA.cxs

opened ChimeraX session  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
ERROR: Could not find a version that satisfies the requirement ChimeraX-
AddH==2.1.3  
ERROR: No matching distribution found for ChimeraX-AddH==2.1.3  
WARNING: You are using pip version 20.2.2; however, version 20.3.1 is
available.  
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.1\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
ERROR: Could not find a version that satisfies the requirement ChimeraX-
AddH==2.1.3  
ERROR: No matching distribution found for ChimeraX-AddH==2.1.3  
WARNING: You are using pip version 20.2.2; however, version 20.3.1 is
available.  
You should consider upgrading via the 'C:\Program Files\ChimeraX
1.1\bin\ChimeraX.exe -m pip install --upgrade pip' command.  
  




OpenGL version: 3.3.0 NVIDIA 431.53
OpenGL renderer: GeForce GTX 1060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Alienware
Model: Alienware 13 R3
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 17,046,663,168
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
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-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
    gdcm: 2.8.8
    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+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added
Component: Unassigned → Tool Shed
Description: modified (diff)
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Could not find a version that satisfies the requirement ChimeraX-AddH==2.1.3

Reported by Michael Weber

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: assigned → closed

Hi Michael,

Thanks for reporting this problem. We believe it is fixed now.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by weberm@…, 5 years ago 

Hi Eric,
thanks for the quick fixing of the issue.
:)
Michael.

Am 10.12.2020 20:15 schrieb ChimeraX:
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