How to do inter/intra protein chain-breaks through command line interface ?

Hi Yoshitaka-san,

Thank you for the great work.

Original AlphaFold2_advanced allows you to do inter protein chain-breaks in the sequence entry:

So you can do something like: AC/DE:FGH

Use / to specify intra-protein chainbreaks (for trimming regions within protein).
Use : to specify inter-protein chainbreaks (for modeling protein-protein hetero-complexes).

How can we do this with your script? Because it only takes one file as fasta file.

Do you create a fasta file like:

 >myinput.fasta
 AC/DE:FGH

And last question, DE:FGH simply means we are docking DE to FGH, am I right?

Thanks and hope to hear from you again.

G.V.

[CYP152N1]

If anyone knows how to use it effectively, please let me know.

I think trim feature is useful for scoring pLDDT and tol of the models with disorder loop. Trimming of low pLDDT region makes the rank of pLDDT will be more accurate. But It might be better that the rescoring average pLDDT performed on another program after the AF2 calculation.

If the model possess disorder loop, tol was not decreased after several recycles.
Trimming of disorder loop might be effective to judge the endpoint of recycling. However, I have never use it.

[gundalav]

Yoshitaka-san, Thank you for the explanation. Very convincing G.V.