jueseph
commented
2 years ago for binder-receptor complexes, you want to use af2_interface_metrics.py rather than af2_metrics.py. however, in order to use this script you will need to combine your pdbs into a silent file using silent_tools https://github.com/bcov77/silent_tools (which requires an installation of pyrosetta).
this script inputs a template for the receptor and puts an initial guess for the binder, as described in this preprint https://www.biorxiv.org/content/10.1101/2022.06.15.495993v1
On Wed, Aug 3, 2022 at 7:12 PM jongseo @.***> wrote:
Hi,
After design protein binder using hallucination.py, I tried to validate results.
According to the tutorials, first I run the trfold_relax.sh,
and then run the af2_metrics.py .
However, the modeling result was implausible especially in the receptor region.
In the case of my receptor, the modeling result was plausible only if the MSA is provided.
I thought that the implausible result of af2_metrics.py might be originated from the modeling without MSA.
So, is there any protocol or alternative way to validate my result ?
Sincerely, jongseo
— Reply to this email directly, view it on GitHub https://github.com/RosettaCommons/RFDesign/issues/12, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABCU55L3GTB32EZ6NZ4C4LVXMRI3ANCNFSM55Q3GYDQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
jongseo-park
Hi,
After design protein binder using hallucination.py, I tried to validate results.
According to the tutorials, first I run the trfold_relax.sh,
and then run the af2_metrics.py .
However, the modeling result was implausible especially in the receptor region.
In the case of my receptor, the modeling result was plausible only if the MSA is provided.
I thought that the implausible result of af2_metrics.py might be originated from the modeling without MSA.
So, is there any protocol or alternative way to validate my result ?
Sincerely, jongseo