Auto-style on 4 chain 120,000 atoms looks bad

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-12.5.1-arm64-arm-64bit
ChimeraX Version: 1.5.dev202208311802 (2022-08-31 18:02:52 UTC)
Description
Auto-style on this 120,000 four chain ryanodine structure 7tdh seems not too useful, all stick, no distinct chain colors.  This is following the documented auto-style rules but I think this should be improved.  It looks much better using the 200000-1000000 atom rules, sphere colored by chain.

Log:
UCSF ChimeraX version: 1.5.dev202208311802 (2022-08-31)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7tdh format mmcif fromDatabase pdb

7tdh title:  
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in open
conformation [more info...]  
  
Chain information for 7tdh #1  
---  
Chain | Description | UniProt  
A B C D | Ryanodine receptor 1,Ryanodine receptor 1,RyR1 | RYR1_RABIT  
  
Non-standard residues in 7tdh #1  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
CA — calcium ion  
ZN — zinc ion  
  

> view orient

[Repeated 1 time(s)]

> save /Users/goddard/Desktop/image1.png supersample 3

> select #1

117532 atoms, 119752 bonds, 100 pseudobonds, 16676 residues, 3 models selected  

> select clear

> show cartoons

> hide atoms

> color bypolymer

> style sphere

Changed 117532 atom styles  

> show atoms

> hide cartoons

> color bychain

> show cartoons

> hide atoms

> show atoms

> style sphere

Changed 117532 atom styles  

> lighting soft




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 10 days 12:42

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
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          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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[goddard@…]

Here is what it looks like by default, and what it looks like with the >200,000 atom autostyle.

[goddard@…]

Added by email2trac

[goddard@…]

Added by email2trac

[pett]

Well, the auto styling "rules" are just heuristics and are meant to be tweaked for scenarios where they don't work well. I'll see what I can do.

[pett]

The ribbon upper limit that Greg added for performance reasons leaves structures < 200,000 atoms but exceeding the ribbon threshold depicted as just sticks, which looks terrible. Changed the heuristic so that such structures get kicked up into the space-filling spheres preset.