Custom a3m and pdb - Scaffolding functional motifs from an EvoDiff-MSA

[JisungJang-AI-BIO]

Hello, thank you for sharing this powerful tool!

I'm trying to generate a new scaffold sequences on the custom a3m and pdb that produced using openfold, but not published on PDB.

However, I could not found how to load PDB from the local path in 'evodiff/conditional_generation_msa.py'.

Q1. How should I change the code to achieve this goal?

Q2. Are you planning to update code to be able to perform this kind of task?

Alternatively, I generated sequences of which length is same to the query sequence using EvoDiff-MSA.
And then, I revert the sequence on motif region of the generated sequence.
In this way, we can generate partly conserved sequences that we wanted.

Although this approach can still achieve the desired results, the differences between models still remained.
It would be glad to be shared your opinion about this approach.