Automatically color bypolymer when large structure opened

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-13.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202306281841 (2023-06-28 18:41:15 UTC)
Description
Make large structure (> 1 million atoms) color by polymer.  Currently they are shown as a single color.  Color bypolymer is very fast so does not increase the time to open much, and the colors help understand the large models.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.7.dev202306281841 (2023-06-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8iyj format mmcif fromDatabase pdb

8iyj title:  
Cryo-EM structure of the 48-nm repeat doublet microtubule from mouse sperm
[more info...]  
  
Chain information for 8iyj #1  
---  
Chain | Description | UniProt  
0 7 | Cilia- and flagella-associated protein 95 | CFA95_MOUSE 1-228  
1 2 | EF-hand domain-containing family member B | EFHB_MOUSE 1-853  
3 4 | Cilia- and flagella-associated protein 53 | CFA53_MOUSE 1-514  
5 6 j1 | Nucleoside diphosphate kinase 7 | NDK7_MOUSE 1-395  
8 | Cilia- and flagella-associated protein 107 | CF107_MOUSE 1-196  
A N1 | Cilia- and flagella-associated protein 141 | CP141_MOUSE 1-101  
A0 A1 A2 A3 A4 A5 | Tektin-1 | TEKT1_MOUSE 1-418  
AA AC AE AG AI AK AM AO BC BE BG BI BK BM BO CC CE CG CI CK CM CO CQ DC DE DG
DI DK DM DO DQ EA EC EE EG EI EK EM EO FA FC FE FG FI FK FM FO GA GC GE GG GI
GK GM GO HA HC HE HG HI HK HM HO IA IC IE IG II IK IM IO JC JE JG JI JK JM JO
JQ KA KC KE KG KI KK KM KO LA LC LE LG LI LK LM LO MA MC ME MG MI MK MM MO NA
NC NE NG NI NK NM NO OA OC OE OG OI OK OM OO PC PE PG PI PK PM PO QC QE QG QI
QK QM QO RC RE RG RI RK RM RO SA SC SE SG SI SK SM TA TC TE TG TI TK TM UA UC
UE UG UI UK UM UO VA VC VE VG VI VK VM VO WA WC WE WG WI WK WM WO | Tubulin
alpha-3 chain | TBA3_MOUSE 1-450  
AB AD AF AH AJ AL AN AP BB BD BF BH BJ BL BN BP CB CD CF CH CJ CL CN CP DB DD
DF DH DJ DL DN DP EB ED EF EH EJ EL EN FB FD FF FH FJ FL FN GB GD GF GH GJ GL
GN HB HD HF HH HJ HL HN HP IB ID IF IH IJ IL IN IP JB JD JF JH JJ JL JN JP KB
KD KF KH KJ KL KN KP LB LD LF LH LJ LL LN LP MB MD MF MH MJ ML MN MP NB ND NF
NH NJ NL NN NP OB OD OF OH OJ OL ON OP PB PD PF PH PJ PL PN PP QB QD QF QH QJ
QL QN QP RD RF RH RJ RL RN RP SB SD SF SH SJ SL SN TB TD TF TH TJ TL TN UB UD
UF UH UJ UL UN VB VD VF VH VJ VL VN WB WD WF WH WJ WL WN WP | Tubulin beta-4B
chain | TBB4B_MOUSE 1-445  
B C | Meiosis-specific nuclear structural protein 1 | MNS1_MOUSE 1-491  
B0 B1 B2 B3 B4 B5 R0 R1 R2 R3 R4 R5 | Tektin-2 | TEKT2_MOUSE 1-430  
C0 C1 C2 C3 C4 C5 C6 S0 S1 S2 S3 S4 S5 S6 S7 S8 S9 | Tektin-3 | TEKT3_MOUSE
1-490  
D K3 | Sperm-associated antigen 8 | SPAG8_MOUSE 1-470  
D0 D1 D2 D3 D4 D5 T0 T1 T2 T3 T4 T5 | Tektin-4 | TEKT4_MOUSE 1-447  
E F N2 | Cilia- and flagella-associated protein 161 | CF161_MOUSE 1-303  
G | Piercer of microtubule wall 2 protein | PIRC2_MOUSE 1-122  
H I J K L M N O7 O8 O9 P8 P9 Z2 Z3 Z4 Z5 | Protein FAM166A | F166A_MOUSE 1-319  
I1 | Cilia- and flagella-associated protein 68 | CFA68_MOUSE 1-166  
J1 J2 J3 J4 J5 | Cilia and flagella-associated protein 77 | A0A087WRI3_MOUSE
1-283  
K1 K2 | Family with sequence similarity 183, member B | D2D553_MOUSE 1-137  
L1 | Cilia- and flagella-associated protein 90 | CFA90_MOUSE 1-182  
M1 M2 M3 M4 | Protein FAM166C | F166C_MOUSE 1-200  
O P Q | RIB43A-like with coiled-coils protein 1 | RIBC1_MOUSE 1-379  
O1 O2 O3 O4 | Dual specificity phosphatase 21 | DUS21_MOUSE 1-189  
O5 O6 T U V | EF-hand domain-containing protein 1 | EFHC1_MOUSE 1-648  
P1 P2 | Testis expressed 49 | Q8CDT5_MOUSE 1-131  
P3 P4 P5 P6 P7 | Testis-expressed sequence 37 protein | TEX37_MOUSE 1-180  
Q1 Q2 Q3 Q4 Q5 | Tektin bundle-interacting protein 1 | TKTI1_MOUSE 1-206  
R S | RIB43A-like with coiled-coils protein 2 | RIBC2_MOUSE 1-377  
U0 U1 U2 U3 U4 U5 U6 U7 U8 U9 V0 V1 V2 V3 V4 V5 V6 V7 V8 V9 W0 W2 W4 W5 W6 W7
| Tektin-5 | TEKT5_MOUSE 1-557  
W X Y Z | EF-hand domain-containing family member C2 | EFHC2_MOUSE 1-750  
X0 X1 X2 X3 | Spermatid-specific manchette-related protein 1 | SMRP1_MOUSE
1-260  
X4 X5 | Protein phosphatase 1 regulatory subunit 32 | PPR32_MOUSE 1-427  
X6 X7 X8 | Testis-specific serine/threonine-protein kinase 6 | TSSK6_MOUSE
1-273  
XA XB XC XD XE XF XG XH | Cilia- and flagella-associated protein 20 |
CFA20_MOUSE 1-193  
Y0 Y1 Y2 Y3 Y4 Y5 | Outer dense fiber protein 3 | ODF3A_MOUSE 1-254  
YA YB YC YD YE YF YG YH | Parkin coregulated gene protein homolog |
PACRG_MOUSE 1-241  
Z1 | Testis, prostate and placenta-expressed protein | TEPP_MOUSE 1-216  
a a6 b c d | Cilia- and flagella-associated protein 45 | CFA45_MOUSE 1-551  
a1 a2 a3 a4 | Uncharacterized protein C10orf82 homolog | CJ082_MOUSE 1-229  
b1 b2 b3 b4 b5 | Coiled-coil domain-containing protein 105 | CC105_MOUSE 1-499  
e f g | Cilia- and flagella-associated protein 52 | CFA52_MOUSE 1-620  
h i j k | Enkurin | ENKUR_MOUSE 1-255  
h1 h2 h3 h4 | Testis-expressed protein 43 | TEX43_MOUSE 1-141  
i1 l m n | Protein Flattop | FLTOP_MOUSE 1-189  
i2 i3 i4 | EF-hand calcium-binding domain-containing protein 6 | EFCB6_MOUSE
1-1516  
o p | Cilia- and flagella-associated protein 210 | CF210_MOUSE 1-547  
q r s | Cilia- and flagella-associated protein 276 | CF276_MOUSE 1-168  
y | Piercer of microtubule wall 1 protein | PIRC1_MOUSE 1-167  
  
Non-standard residues in 8iyj #1  
---  
GDP — guanosine-5'-diphosphate  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
  




OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 512.0.0.0.0
      OS Loader Version: 577~170
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (22F82)
      Kernel Version: Darwin 22.5.0
      Time since boot: 13 days, 14 hours, 39 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46
    ChimeraX-AtomicLibrary: 10.0.7
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202306281841
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NIHPresets: 1.1.9
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.30
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.40.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.3.16
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.8.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.1.0
    pyproject-hooks: 1.0.0
    PyQt6: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.6.3
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7

[Tom Goddard]

Done.

I've attached an image for an example microtubule structure 8iyj comparing single color to color bypolymer.

[Tom Goddard]

Image comparing color bypolymer to single color for 8iyj

[Tom Goddard]

The time for opening 8iyj single colors was 4.6 seconds and with color bypolymer 4.7 seconds (2% slower) on my 2017 iMac.

[Elaine Meng]

Is the only criterion for this the number of atoms?  Would it be reasonable to also do this for 250 chains or more?  The reason I ask is that currently we have this as the largest auto-styling category:

\u2022 250+ chains and/or 1,000,000+ atoms: all atoms as spheres (space-filling), coloring by model, soft lighting (except if \u2265 300,000 atoms, ambient shadows from 16 instead of 64 directions)

[goddard@…]

Yes, the new color by polymer is for models with more than 250 chains or more than 1 million atoms.  I just added it for the largest auto-styling category, I did not make a new category.  Sorry I was not clear about that.