SortedDIct.iloc deprecated

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1rc202009032250 (2020-09-03 22:50:43 UTC)
Description
Got a warning "sorted_dict.iloc is deprecated" in core/commands/colorarg.py line 326

Jupyter QtConsole 4.7.4

Current ChimeraX session available as 'session'.

Python 3.7.8 (default, Sep  6 2020, 04:00:42) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.15.0 -- An enhanced Interactive Python. Type '?' for help.

m = session.models.list()[0]

len(m.residues)
Out[2]: 382

from chimerax.isolde.atomic.building.build_utils import add_amino_acid_residue

from chimerax.atomic import selected_residues

add_amino_acid_residue(m, 'PRO', next_res=selected_residues(session)[0])
/Users/goddard/Desktop/ChimeraX rc Sep 6 2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/colorarg.py:326: DeprecationWarning: sorted_dict.iloc is deprecated. Use SortedDict.keys() instead.
  color_name = color_dict.iloc[i]
Out[5]: <chimerax.atomic.molobject.Residue at 0x13917bed0>


Log:
UCSF ChimeraX version: 1.1rc202009032250 (2020-09-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3fhr format mmcif fromDatabase pdb

3fhr title:  
High resolution crystal structure of mitogen-activated protein kinase-
activated protein kinase 3 (MK3)-inhibitor complex [more info...]  
  
Chain information for 3fhr #1  
---  
Chain | Description  
A | MAP kinase-activated protein kinase 3  
  
Non-standard residues in 3fhr #1  
---  
P4O —
2-(2-quinolin-3-ylpyridin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-C]pyridin-4-one  
  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/grako/grammars.py:16: DeprecationWarning: Using or importing the ABCs
from 'collections' instead of from 'collections.abc' is deprecated since
Python 3.3,and in 3.9 it will stop working  
from collections import defaultdict, Mapping  

> select /A:33

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui tool show Shell

/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ipykernel/iostream.py:14: DeprecationWarning: the imp module is
deprecated in favour of importlib; see the module's documentation for
alternative uses  
from imp import lock_held as import_lock_held  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ipykernel/datapub.py:5: DeprecationWarning: ipykernel.datapub is
deprecated. It has moved to ipyparallel.datapub  
warnings.warn("ipykernel.datapub is deprecated. It has moved to
ipyparallel.datapub", DeprecationWarning)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ipykernel/serialize.py:7: DeprecationWarning: ipykernel.serialize is
deprecated. It has moved to ipyparallel.serialize  
warnings.warn("ipykernel.serialize is deprecated. It has moved to
ipyparallel.serialize", DeprecationWarning)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ipykernel/pickleutil.py:8: DeprecationWarning: ipykernel.pickleutil
is deprecated. It has moved to ipyparallel.  
warnings.warn("ipykernel.pickleutil is deprecated. It has moved to
ipyparallel.", DeprecationWarning)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ipykernel/codeutil.py:17: DeprecationWarning: ipykernel.codeutil is
deprecated since IPykernel 4.3.1. It has moved to ipyparallel.serialize  
warnings.warn("ipykernel.codeutil is deprecated since IPykernel 4.3.1. It has
moved to ipyparallel.serialize", DeprecationWarning)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/ipykernel/iostream.py:66: DeprecationWarning: zmq.eventloop.ioloop is
deprecated in pyzmq 17. pyzmq now works with default tornado and asyncio
eventloops.  
self.io_loop = IOLoop(make_current=False)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/jupyter_client/session.py:813: DeprecationWarning: Accessing zmq
Socket attribute recv_multipart on BackgroundSocket  
msg_list = socket.recv_multipart(mode, copy=copy)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/jupyter_client/session.py:813: DeprecationWarning: Accessing zmq
Socket attribute recv_multipart on BackgroundSocket  
msg_list = socket.recv_multipart(mode, copy=copy)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/jupyter_client/session.py:813: DeprecationWarning: Accessing zmq
Socket attribute recv_multipart on BackgroundSocket  
msg_list = socket.recv_multipart(mode, copy=copy)  

> hide sel cartoons

> select clear

> hide cartoons

> show atoms

> select /A:33

9 atoms, 8 bonds, 1 residue, 1 model selected  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/jupyter_client/session.py:813: DeprecationWarning: Accessing zmq
Socket attribute recv_multipart on BackgroundSocket  
msg_list = socket.recv_multipart(mode, copy=copy)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/jupyter_client/session.py:813: DeprecationWarning: Accessing zmq
Socket attribute recv_multipart on BackgroundSocket  
msg_list = socket.recv_multipart(mode, copy=copy)  
/Users/goddard/Desktop/ChimeraX rc Sep 6
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/jupyter_client/session.py:813: DeprecationWarning: Accessing zmq
Socket attribute recv_multipart on BackgroundSocket  
msg_list = socket.recv_multipart(mode, copy=copy)  




OpenGL version: 4.1 ATI-3.10.16
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G2021)
      Kernel Version: Darwin 19.6.0
      Time since boot: 12 days 20:21

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1rc202009032250
    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-ISOLDE: 1.0.2
    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
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    openvr: 1.12.501
    packaging: 20.4
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    Pillow: 7.1.2
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    pkginfo: 1.5.0.1
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    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
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    webcolors: 1.11.1
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