For antibody antigen modeling using the native version of HADDOCK3, I refer to the Antibody Antigen Modeling Using the Native Version of HADDOCK3 tutorial (Antibody-antigen modelling tutorial using a local version of HADDOCK3 – Bonvin Lab). Creating a HADDOCK3 profile for defining the docking workflow, no reference is given, how do I set up the caprieval step(s)?
Hi holly,
The [caprieval] module is mostly used for benchmarking purposes (if you have a reference file), or will use as reference the best scoring models.
Tt also allows to generate the final plots during the post-processing steps (in the analysis directory).
If you do not provide any reference file, just run [caprieval] using default parameters.
Cheers
Is it sufficient to leave the next line under [caprieval] empty and unprocessed as shown in the picture?
Yes, if you do not have a reference structure.
In that case, the lowest energy structure will be used as reference for the plots
Thank you very much for your explanation, it has helped me a lot