search

RosettaCommons / RFDesign

Protein hallucination and inpainting with RoseTTAFold
Other
234 stars 67 forks source link

Workflow for resultant inpainting models #30

Closed jadolfbr closed 1 year ago

jadolfbr commented 1 year ago

I think this code should maybe have a wiki attached to it to add general knowledge? I have been able to run and get at least something out. The PDBs do not inlclude rotamers/sidechains, but do include the identity of the residues. What is your general workflow for then incorporating these sequences and modeling the side chains? Do you have scripts available that you could share that does this?

jueseph commented 1 year ago

Hi Jared,

Sorry this isn't easier to use. Partly we are trying to put together newer versions of the software to release that are more powerful, and so figured we'd support those more seriously when they're released.

For this version of hallucination/inpainting, we use the trfold_relax.sh script (see https://github.com/RosettaCommons/RFDesign/tree/main/scripts) to add sidechains (using Rosetta).

I assumed Github issues would provide a forum for people to share notes on how to run things. Wiki is a good idea too. Do you have a suggested software/service that would plug in to Github?

Jue

On Thu, Sep 22, 2022 at 8:51 AM Jared Adolf-Bryfogle < @.***> wrote:

I think this code should maybe have a wiki attached to it to add general knowledge? I have been able to run and get at least something out. The PDBs do not inlclude rotamers/sidechains, but do include the identity of the residues. What is your general workflow for then incorporating these sequences and modeling the side chains? Do you have scripts available that you could share that does this?

— Reply to this email directly, view it on GitHub https://github.com/RosettaCommons/RFDesign/issues/30, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABCU5Y3VXHKRQGZMVXSDYDV7R57HANCNFSM6AAAAAAQTGE5FA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

jadolfbr commented 1 year ago

Hey Joe,

I think for a repo, you can select to have a wiki and it will be handled by Github. I think it's a repo option in the settings. It's really useful. There are some docs to it. https://carldesouza.com/creating-a-github-wiki-documentation-for-your-repository/

I did find the TRRosetta relax script and also realized if I just read and then dump a PDB in PyRosetta it will add side chains and pack them to the CB. I think this information is just missing from the inpainting docs, but the relax script is in the hallucination docs.