How to generate cyclic backbone with rfdiffusion2

[breadbread1984]

I run rf_diffusion/run_inference.py to generate a binder in chain B for target protein in chain A with parameters contigmap.has_termini=[true, false] inference.denoiser=cyclic inference.cyc_chains=['B']. but I still cannot get a cyclic binder. is there any othre necessary parameters for cyclic binder?

[rclune]

Which config file are you pulling these settings from? I'm having trouble finding a configuration file in RFdiffusion2 that defines a cyc_chains option.

Out of the ones provided in RFdiffusion2/rf_diffusion/config, only aa.yaml and aa_ppi.yaml should be used. The other provided config files have either project-specific configuration settings or settings that were not fully incorporated into RFdiffusion2.

RFdiffusion has some examples for generating cyclic oligomers, these sound the most relevant to your project.

[breadbread1984]

thank you for your kindly reply. I will switch to rfdiffusion1 for cyclic binder generation