Alphafold error prediction GUI does not guess PAE file name

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202401221910 (2024-01-22 19:10:45 UTC)
Description
The AlphaFold error prediction gui is not able to guess the PAE file name from the structure file name for results computed by AlphaFold 2.3.2.  The structure file name is

unrelaxed_model_1_multimer_v3_pred_0.cif 

and the PAE json file name is

pae_model_1_multimer_v3_pred_0.json 

in output from AlphaFold 2.3.2 run on the UCSF Wynton cluster.



Log:
UCSF ChimeraX version: 1.8.dev202401221910 (2024-01-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/goddard/ucsf/data/alphafold/cncalcium_01613_06362/unrelaxed_model_1_multimer_v3_pred_0.cif

Chain information for unrelaxed_model_1_multimer_v3_pred_0.cif #1  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/goddard/ucsf/data/alphafold/cncalcium_01613_06362/confidence_model_1_multimer_v3_pred_0.json

JSON file
"/Users/goddard/ucsf/data/alphafold/cncalcium_01613_06362/confidence_model_1_multimer_v3_pred_0.json"
is not AlphaFold predicted aligned error data, expected a top level list  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/goddard/ucsf/data/alphafold/cncalcium_01613_06362/pae_model_1_multimer_v3_pred_0.json




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

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      Kernel Version: Darwin 23.2.0
      Time since boot: 36 days, 1 hour, 59 minutes

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    Apple M2 Ultra:

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          UI Looks like: 1920 x 1080 @ 60.00Hz
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          Online: Yes
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[Tom Goddard]

The same failure to guess the PAE file happens if the the .pdb structure file is opened. Also the AlphaFold 2.3.2 contains the same .pkl file which also has the PAE data

result_model_1_multimer_v3_pred_0.pkl

It is probably preferable to read the json file though since the pkl file can be extremely large (e.g. 11 Gbytes for a 4700 amino acid dimer prediction! while the json is 100 Mbytes).

[Tom Goddard]

I see the problem is that the code looks for a long matching file suffix (without the extension) but only uses that if there is exactly one file with the longest suffix. And now the .json and .pkl files have the same length matching suffix

unrelaxed_model_1_multimer_v3_pred_0.cif
unrelaxed_model_1_multimer_v3_pred_0.pdb
pae_model_1_multimer_v3_pred_0.json
result_model_1_multimer_v3_pred_0.pkl

I also want to prefer the json file since it is much smaller.

[Tom Goddard]

Fixed.

There were three different problems. One is that the suffxes of the json and pkl files are the same length and so it decided it was a tie and didn't suggest any file. I made it prefer json over pkl. But there is another json file with the same suffix length that is the plddt scores.

confidence_model_1_multimer_v3_pred_0.json

I made it ignore the json files starting with "confidence_". Lastly the common suffix code was wrong and was always treating the whole filename as matching because of using indexing -0 instead of -1 to read the last character of a string.