Opened 5 years ago

Closed 5 years ago

#3968 closed defect (fixed)

map save error

Reported by: r.frank@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Saving a map that has zeros outside the mask (using zoneMask( is not working/giving an error. Here is what I did:
1) Loaded a map (#1) and model (#2).
2) Selected the model
3) Ran volume zone command (volume zone #1 nearAtoms sel range 7 newMap true) to make a new map (#3)
4) Tried to save zoned map (save jnk.mrc format mrc models #3 zoneMask true).

I get an error in red reading "Expected a keyword". If I omit the zoneMask flag, the save commond works. Please can help me save a masked map.

Many thanks,

Rene

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

> open /Users/fbsrfr/Desktop/tmp_iglur_subtomo_str.cxs format session

Log from Fri Sep 4 09:32:17 2020Some installed bundles are out of date. Please
update the following bundles:

  * UI to version 1.2.1 (currently 1.0)
  * UI to version 1.2 (currently 1.0)

  
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/maps/FSCout_maskname_mask_sym2_it_16_finalsharpref_1000.mrc

Opened FSCout_maskname_mask_sym2_it_16_finalsharpref_1000.mrc, grid size
96,96,96, pixel 5.97, shown at level 0.237, step 1, values float32  

> volume #1 color #b2b2b2fe

> volume #1 color #b2b2b2f2

> volume #1 color #b2b2b2f1

> volume #1 color #b2b2b2ed

> volume #1 color #b2b2b2e8

> volume #1 color #b2b2b2e6

> volume #1 color #b2b2b2e4

> volume #1 color #b2b2b2e0

> volume #1 color #b2b2b2de

> volume #1 color #b2b2b2db

> volume #1 color #b2b2b2d9

> volume #1 color #b2b2b2d7

> volume #1 color #b2b2b2cc

> volume #1 color #b2b2b2c8

> volume #1 color #b2b2b2c7

> volume #1 color #b2b2b2c4

> volume #1 color #b2b2b2c3

> volume #1 color #b2b2b2c1

> volume #1 color #b2b2b2bf

> volume #1 color #b2b2b2b8

> volume #1 color #b2b2b2b3

> volume #1 color #b2b2b2b1

> volume #1 color #b2b2b2ad

> volume #1 color #b2b2b2ab

> volume #1 color #b2b2b2a9

> volume #1 color #b2b2b2a6

> volume #1 color #b2b2b2a4

> volume #1 color #b2b2b2a0

> volume #1 color #b2b2b29d

> volume #1 color #b2b2b29c

> volume #1 color #b2b2b298

> volume #1 color #b2b2b297

> volume #1 color #b2b2b295

> volume #1 color #b2b2b294

> open
> /Users/fbsrfr/Dropbox/D_Work/Internal/cryoCLEM_Psd95_manuscript/maps/3kg2.pdb

3kg2.pdb title:  
AMPA subtype ionotropic glutamate receptor In complex with competitive
antagonist ZK 200775 [more info...]  
  
Chain information for 3kg2.pdb #2  
---  
Chain | Description  
A B C D | glutamate receptor 2  
  
Non-standard residues in 3kg2.pdb #2  
---  
BMA — β-D-mannose  
NAG — N-acetyl-D-glucosamine  
ZK1 —
{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic
acid
([[3,4-dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluoromethyl)-1(2H)-quinoxalinyl]methyl]phosphonic
acid)  
  

> volume #1 level 0.2669

> volume #1 level 0.2933

> volume #1 level 0.2801

> set bgColor white

> set bgColor black

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/fbsrfr/Desktop/movie3.mp4

Movie saved to /Users/fbsrfr/Desktop/movie3.mp4  
  

> background white

Unknown command: background white  

> set bgColor white

> save /Users/fbsrfr/Desktop/image9.png supersample 3

> lighting full

> lighting shadows false

> lighting full

> save /Users/fbsrfr/Desktop/image10.png supersample 3

> save /Users/fbsrfr/Desktop/tmp_iglur_subtomo_str.cxs includeMaps true

opened ChimeraX session  

> select #2

22686 atoms, 23200 bonds, 16 pseudobonds, 3134 residues, 2 models selected  

> volume zone #1 nearAtoms sel range 7 newMap true

> save jnk.mrc format mrc models #3 zoneMask true

Expected a keyword  




OpenGL version: 4.1 INTEL-12.10.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Intel Core i5
      Processor Speed: 2.3 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: 16 GB
      Boot ROM Version: 428.0.0.0.0
      SMC Version (system): 2.43f6

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G6032)
      Kernel Version: Darwin 18.7.0
      Time since boot: 2 days 6:56

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        PL2483H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1156292263699
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort
        PL2483H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1156280844710
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

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
    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
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    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 (6)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → map save error

comment:2 by Eric Pettersen, 5 years ago

Resolution: → not a bug
Status: assigned → closed

Hi Rene,

The keyword is 'maskZone', not 'zoneMask'.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by R.Frank@…, 5 years ago 

Hi Eric,

That was was typo - sorry. Alas, I get the same error with maskZone. Here are my commands again:

volume zone #1 nearAtoms sel range 7 newMap true
save jnk.mrc format mrc models #3 maskZone true

All the best,

Rene

comment:4 by Eric Pettersen, 5 years ago

Cc: Eric Pettersen added
Resolution: not a bug
Status: closed → reopened

Tom,

All save keywords except for "models" are currently being restricted to the .cmap format. Looking at the 'save' documentation, it seems that 'step', 'region', and 'maskZone' should be applicable to all formats. Is that correct? If so, then one of us needs to update the save-keyword information. I can do that if it is in fact correct to do so...

--Eric

comment:5 by Tom Goddard, 5 years ago

Cc: Tom Goddard added; Eric Pettersen removed
Owner: changed from Tom Goddard to Eric Pettersen
Status: reopened → assigned

You are right Eric that step, region, and maskZone options apply to saving all map formats. Before you changed the save command to allow different options for different formats that is how it worked. Since you converted the code, how about you fix it so that those 3 options apply to saving all map formats.

comment:6 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: assigned → closed

Hi Rene,

This will work in tomorrow's daily build. Until then, you could save a .cmap file instead (and, if needed, read that back into ChimeraX and then write out a .mrc file).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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