Alphafold interfaces: PAE not opened

[bruno.haymele@…]

The following bug report has been submitted:
Platform:        Linux-6.1.0-5-amd64-x86_64-with-glibc2.40
ChimeraX Version: 1.9.dev202409012236 (2024-09-01 22:36:02 UTC)
Description
Here's a corrected version of your text with improved English:

---

I manually compiled a multi-sequence FASTA file and used it to generate the AF3 JSON input with the following command:

```
alphafold dimers seqs.fasta outputJson scmc_af3.json
```

Next, I generated the models using the AF3 server. Afterward, I decompressed everything and ran:

```
alphafold interfaces folder/
```

As soon as I open any of the dimes, it reports missing data with the following error:

"Structure nalp5_human_nalp5_human #1 does not have PAE data opened."

Interestingly, the PAE plot still opens.

Ps: sorry for the blank report, my finger slipped.

Log:
> alphafold dimers
> /home/arfalas/working/scmc_new/uniprotkb_xref_complexportal_CPX_2210_2024_09_03.fasta
> outputJson scmc_af3.json

28 dimers with lengths 298-2400.  
Estimated prediction time 20 hours 56 minutes using Nvidia 3090 GPU.  
7 monomer sequences with lengths 149-1200:  
KHDC3_HUMAN (217), NALP2_HUMAN (1062), NALP5_HUMAN (1200), NALP7_HUMAN (980),
OOEP_HUMAN (149), PADI6_HUMAN (694), TLE6_HUMAN (572)  

> alphafold interfaces working/scmc_new/fo

7 of 28 dimers have 10 or more confident residue interactions  
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.  
Sequences| Models| Confident pairs| #Res1|  #Res2 | nalp5_human_nalp5_human | 5 | 35 | 17 | 18   
---|---|---|---|---  
nalp5_human_tle6_human | 5 | 11 | 6 | 6   
ooep_human_khdc3_human | 5 | 23 | 10 | 14   
ooep_human_ooep_human | 5 | 23 | 14 | 14   
ooep_human_tle6_human | 5 | 32 | 13 | 17   
padi6_human_padi6_human | 5 | 86 | 46 | 45   
tle6_human_nalp2_human | 5 | 34 | 20 | 17   
Open best. Hide or show disordered loops (pLLDT <= 50).  

> open working/scmc_new/fo/fold_nalp5_human_nalp5_human_model_2.cif

Chain information for fold_nalp5_human_nalp5_human_model_2.cif #1  
---  
Chain | Description  
A B | .  
  
Computing secondary structure  

> rename last-opened nalp5_human_nalp5_human

> color last-opened bypolymer

> select
> /A:966,969,973,976,993,994,995,998,999,1002,1005,1023,1026,1027,1030,1031,1033/B:966,969,973,976,993,994,995,998,999,1002,1005,1023,1026,1027,1030,1031,1033,1034
> & last-opened

293 atoms, 271 bonds, 35 residues, 1 model selected  

> alphafold pae last-opened file
> working/scmc_new/fo/fold_nalp5_human_nalp5_human_full_data_2.json plot false

> alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4
> maxPae 5

Structure nalp5_human_nalp5_human #1 does not have PAE data opened  

> close

> alphafold interfaces working/scmc_new/fo

7 of 28 dimers have 10 or more confident residue interactions  
spanning <= 4 Angstroms with predicted aligned error <= 5 Angstroms.  
Sequences| Models| Confident pairs| #Res1|  #Res2 | nalp5_human_nalp5_human | 5 | 35 | 17 | 18   
---|---|---|---|---  
nalp5_human_tle6_human | 5 | 11 | 6 | 6   
ooep_human_khdc3_human | 5 | 23 | 10 | 14   
ooep_human_ooep_human | 5 | 23 | 14 | 14   
ooep_human_tle6_human | 5 | 32 | 13 | 17   
padi6_human_padi6_human | 5 | 86 | 46 | 45   
tle6_human_nalp2_human | 5 | 34 | 20 | 17   
Open best. Hide or show disordered loops (pLLDT <= 50).  

> open working/scmc_new/fo/fold_nalp5_human_tle6_human_model_4.cif

Chain information for fold_nalp5_human_tle6_human_model_4.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> rename last-opened nalp5_human_tle6_human

> color last-opened bypolymer

> select /A:536,537,540,596,637,668/B:158,159,163,164,166,167 & last-opened

120 atoms, 120 bonds, 12 residues, 1 model selected  

> alphafold pae last-opened file
> working/scmc_new/fo/fold_nalp5_human_tle6_human_full_data_4.json

> alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0
> maxPae 5.0

Structure nalp5_human_tle6_human #1 does not have PAE data opened  

> color #1 lightgray ribbons

> alphafold contacts #1/A toAtoms #1/B distance 4

Structure nalp5_human_tle6_human #1 does not have PAE data opened  




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File attachment: 2024-09-03-131111_1917x1055_scrot.png

2024-09-03-131111_1917x1055_scrot.png​

[bruno.haymele@…]

Added by email2trac

[pett]

Reported by Bruno Hay Mele

[Tom Goddard]

Fixed in daily build dated Sept 3, 2024 or newer.

I broke the alphafold pae command file option when making a change 2 weeks ago (August 21) when I added code to make sure an error was issued if no structure was associated with the PAE data. The line of code that assigned the opened PAE data to the structure was indented incorrectly and so was not executed. Fixed the indentation.