Index error

[jimfeng9705]

I encountered this error:
IndexError: index 855 is out of bounds for axis 1 with size 805.

I attached the crosslink csv file.
alphalink.csv

[jimfeng9705]

The fasta file is attached here.
fasta.txt

[lhatsk]

Sorry, this went under. Your chain A is only 657 residues long, how come they are crosslinks at residue position 933? There seems to be something wrong with your FASTA / crosslinking data alignment.

615 A 933 A 0.05

[jimfeng9705]

Thanks for clarifying! I will try it again. Two more questions: 1. shall I use all crosslinks combined from various runs? Would more crosslinks help guide the modeling? 2. The AlphaLink 2 models seem to have lower ptm and iptm scores than AlphaFold models. I tried to use higher recycle number such as 50. What else shall I try to do? Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: lhatsk ***@***.***> Sent: Tuesday, October 8, 2024 3:31:29 AM To: Rappsilber-Laboratory/AlphaLink2 ***@***.***> Cc: Changjian Feng ***@***.***>; Author ***@***.***> Subject: Re: [Rappsilber-Laboratory/AlphaLink2] Index error (Issue #31) [EXTERNAL] Sorry, this went under. Your chain A is only 657 residues long, how come they are crosslinks at residue position 933? There seems to be something wrong with your FASTA / crosslinking data alignment. 615 A 933 A 0.05 — Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BBIHPOOPLY3SCA4NT4AL4DTZ2OQ7DAVCNFSM6AAAAABNE273K6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJZGM2DENBQGY>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[lhatsk]

1. shall I use all crosslinks combined from various runs? Would more crosslinks help guide the modeling?

I would use all crosslinks. In general, more crosslink information should help.

2. The AlphaLink 2 models seem to have lower ptm and iptm scores than AlphaFold models. I tried to use higher recycle number such as 50. What else shall I try to do?

It's hard to say what's going on. How well are the crosslinks explained by the AlphaFold models? Is it a large target? Many chains? Disordered regions? I would go with more sampling instead of more recycling. You could also try v2 weights vs v3 weights.