Hey everyone, hope you are doing well. I'm starting a few runs with

alphafold

, I'm working with a protein complex (3 proteins). I have the complex in a single

fasta

file, inside the file I have the common format:

>sequence_id_1
sequence
>sequence_id_2
...

I'm preparing the

samplesheet.csv

, so in this case I wonder if I should edit this format in some way, for example, in other repositories that work with AF-multimer, to specify a complex you should edit the

fasta

file as follow:

>complex
sequence_id_1:sequence_id_2:sequence_id_3

Should I perform any modification to my current

fasta

file? Any comment is more than welcome! Thank to all the team

Hi Mauricio, The proteinfold pipeline uses multiline fasta files, the first case you have written. When you set

-alphafold2_model_preset multimer

it will process them appropriately

Great! Thank you for clarify it!