Changes for AlphaFold3 PAE broke MOLEonline json reader

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-12.7.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
opening MoleOnline json file gives error about expecting AlphaFold PAE 

Following our click-to-execute tutorial (for example) with the Mole Online json file provided with that tutorial gives an error at the step of opening the Mole Online json file.  See Log contents

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html

Opened https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html  

> open 1bl8

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description | UniProt  
A B C D | PROTEIN (POTASSIUM CHANNEL PROTEIN) | KCSA_STRLI 23-119  
  
Non-standard residues in 1bl8 #1  
---  
K — potassium ion  
  

> hide #1

> cartoon style width .5 thickness .5

> set bgColor light cyan

> graphics silhouettes true depthJump .01

> camera ortho

> open /Users/meng/Desktop/molepore-1bl8.json

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open /Users/meng/Desktop/molepore-1bl8.json format pae structure #1  




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

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 7459.141.1.701.1

Software:

    System Software Overview:

      System Version: macOS 12.7.5 (21H1222)
      Kernel Version: Darwin 21.6.0
      Time since boot: 7 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[Elaine Meng]

Sorry filed ticket before I realized that it still works OK if you add "format mole" ... so maybe the change is that the default interpretation of json changed from mole to pae. I just didn't know about the change or realize it would break the tutorial.

[Tom Goddard]

I've added to the error message that appears when you try to open a MOLE json file without specifying the format the text

If you are trying to open a JSON file that is not AlphaFold PAE data
then you need to specify the format such as 

    open mole_channels.json format mole

Unfortunately many file formats use JSON with a .json extension. I think AlphaFold PAE is more commonly opened in ChimeraX so I made it the default. The ChimeraX "open" command only looks at the file suffix so it has no way to decide what file type a *.json is. If we get more *.json formats one trick we could do is define a default *.json file reader that inspects the first line of the file and dispatches to the right JSON file reader. I don't think we've reached the need for that yet.