splitbyzone

[marta.perez@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-47-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202104240152 (2021-04-24 01:52:36 UTC)
Description
(Describe the actions that caused this problem to occur here)
volume splitbyzone comand doesn't get the uncolor zones (those should also be appearing, according to the help page I guess?), and just the color ones are shown. 

thanks a lot!!
Maybe I should just update the chim version where is already fix?


Log:
UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/mpillana/KR5_SEPT_2020/RD/MAPS/FACETS/kr5_7401_postrpocess_v2_facet.mrc

Opened kr5_7401_postrpocess_v2_facet.mrc as #1, grid size 541,541,486, pixel
1.38, shown at level 0.123, step 4, values float32  

> volume #1 step 1

> open "/home/mpillana/KR5_SEPT_2020/RD/MAPS/PDB/kr5_final_v1_dssp (copy).cif"
> format mmcif

Chain information for kr5_final_v1_dssp (copy).cif #2  
---  
Chain | Description  
A B C D E F G H I J K L | ?  
M | ?  
N | ?  
O P | ?  
  

> hide atoms

> show cartoons

> sym #2 I,222r contact 20 copies true

> close #3

> sym #2 I,222r contact 20 copies false

> show #!2 models

> sym #2 I,222r contact 100 copies false

> lighting simple

> color zone #1 near #2 distance 2 update true

> show #!1 models

> hide #!2 models

> unsym #2

Unknown command: unsym #2  

> sym clear #2

> select #2/a-L

89229 atoms, 91789 bonds, 11156 residues, 1 model selected  

> select #2/A-L

89229 atoms, 91789 bonds, 11156 residues, 1 model selected  

> color #1 blue

> select clear

> hide #!1 models

> show #!2 models

> select #2/A-L

89229 atoms, 91789 bonds, 11156 residues, 1 model selected  

> color sel cornflower blue

> select #2/M

3646 atoms, 3728 bonds, 471 residues, 1 model selected  

> color sel hot pink

> select #2/N

1925 atoms, 1961 bonds, 244 residues, 1 model selected  

> color sel yellow

> select #2/O-P

2838 atoms, 2932 bonds, 2 pseudobonds, 366 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark orange

> select clear

> sym #2 I,222r contact 100 copies true

> show #!1 models

> color #1 #888a85 models

[Repeated 1 time(s)]

> color zone #1 near #3 distance 2 update true

> volume #1 level 0.07913

> volume #1 step 2

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> graphics silhouettes false

> volume gaussian #1 sDev 1

Opened kr5_7401_postrpocess_v2_facet.mrc gaussian as #4, grid size
541,541,486, pixel 1.38, shown at step 1, values float32  

> volume #4 color #888a85

> volume #4 level 0.0222

> volume #4 level 0.03523

> lighting simple

[Repeated 1 time(s)]

> color zone #4 near #3 distance 2 update true

> volume #4 color #ef2929

> color zone #4 near #3 distance 2 update true

> lighting soft

> ui tool show "Side View"

> camera

Camera parameters:  
type: mono  
position: 106.44 -651.77 -1393  
view direction: -0.085053 0.41783 0.90453  
field of view: 30 degrees  

> camera ortho

> lighting simple

> lighting

Intensity: 1  
Direction: 0.577,-0.577,-0.577  
Color: 100,100,100  
Fill intensity: 0.5  
Fill direction: -0.2,-0.2,-0.959  
Fill color: 100,100,100  
Ambient intensity: 0.4  
Ambient color: 100,100,100  
Depth cue: 1, start 0.5, end 1, color 100,100,100  
Shadow: False (depth map size 2048, depth bias 0.005)  
Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01)  

> view

> graphics silhouettes true

> graphics silhouettes false

> lighting depthcueStart 0.8

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> lighting depthCueStart 0.8 depthCueEnd 1

> lighting depthCueStart 0.6 depthCueEnd 1

> lighting depthCueStart 0.2 depthCueEnd 1

> lighting simple

> lighting full

[Repeated 1 time(s)]

> lighting

Intensity: 0.7  
Direction: 0.577,-0.577,-0.577  
Color: 100,100,100  
Fill intensity: 0.3  
Fill direction: -0.2,-0.2,-0.959  
Fill color: 100,100,100  
Ambient intensity: 0.8  
Ambient color: 100,100,100  
Depth cue: 1, start 0.5, end 1, color 100,100,100  
Shadow: True (depth map size 2048, depth bias 0.005)  
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)  

> lighting shadows false

> lighting shadows true

> lighting simple

> ui tool show "Map Eraser"

> hide #!4 models

> select #5

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,-8.431,0,1,0,20.287,0,0,1,214.68

> view

> view matrix models #5,1,0,0,-32.412,0,1,0,77.549,0,0,1,357.93

> view matrix models #5,1,0,0,-50.017,0,1,0,55.78,0,0,1,358.63

> show #!4 models

> view matrix models #5,1,0,0,-2.4214,0,1,0,120.07,0,0,1,346.02

> view matrix models #5,1,0,0,-9.8464,0,1,0,130.29,0,0,1,341.07

> view matrix models #5,1,0,0,-1.3415,0,1,0,112.16,0,0,1,349.98

> view matrix models #5,1,0,0,3.3992,0,1,0,126.65,0,0,1,342.53

> view matrix models #5,1,0,0,-7.3585,0,1,0,130.99,0,0,1,340.64

> view matrix models #5,1,0,0,8.6412,0,1,0,124.85,0,0,1,343.29

> volume erase center

Missing or invalid "volumes" argument: invalid density maps specifier  

> volume erase #4 center 8.6412,124.85,343.29 radius 246.97 outside true

> volume copy #4 subregion 88,102,176,448,462,485

Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy as #6, grid size
361,361,310, pixel 1.38, shown at step 1, values float32  

> hide #!3 models

> select clear

> color zone #6 near #3 distance 2 update true

> lighting full

> volume #6 level 0.02815

> lighting simple

> volume #6 level 0.01993

> volume #6 level 0.02588

> volume erase #6 center 0,0,0 radius 380 outside true

> lighting full

> lighting shadows false

> lighting shadows true

> graphics silhouettes true

> graphics silhouettes false

> volume #6 level 0.01937

> volume #6 level 0.0239

> volume erase #6 center 0,0,0 radius 290 outside false

> lighting depthCueStart 0.8 depthCueEnd 1

> show #!2 models

> hide #!6 models

> show #!6 models

> transparency #6.1 50

> transparency #6.1 0

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 12
atomic models, 1 maps.  

[Repeated 1 time(s)]

> volume splitbyzone #6

Volume kr5_7401_postrpocess_v2_facet.mrc gaussian copy #6 does not have zone
coloring  

> color zone #6 near #3 distance 2 update true

> volume splitbyzone #6

Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 0 as #7.1, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 1 as #7.2, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 2 as #7.3, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 3 as #7.4, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 4 as #7.5, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!7 models

> show #!6 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> help help:contact.html




OpenGL version: 3.3.0 NVIDIA 440.100
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP Pavilion Laptop 14-ce0xxx
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G         11G        1.8G        148M        2.7G        4.1G
	Swap:          2.0G        749M        1.3G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)	
	Subsystem: Hewlett-Packard Company UHD Graphics 620 [103c:84ba]	
	Kernel driver in use: i915
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.1.1
    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: 1.18
    ChimeraX-AtomicLibrary: 3.2
    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-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202104240152
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.2.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.1
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.3
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2
    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
    ChimeraX-ModelPanel: 1.1
    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
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    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: 1.5
    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: 1.8
    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: 5.0.7
    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: 0.17
    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: 1.1.1
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
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    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: 1.2.0

[Eric Pettersen]

Essentially duplicate or predecessor of #4613