Score patching

Rosetta uses a combination of score terms to calculate energy value for a given pose. Rosetta distributions provides several standrdised and tested sets of scoring terms and respective weights. The standard weights may be changed with a patching mechanism. an example is given below

Using rms as a Rosetta score

This example shows how to add crmsd additional score term to Rosetta energy function. The procedure is quite easy, just follow the steps

  1. preape a patch file

A patch file contains the name of a score term and its weight, e.g.

rms_energy = 1.0

  1. Turn on the patch in the appropriate stages of ab-initio protocol by adding the following lines to a flag file that is used to ab-initio protocol:

-abinitio::stage2_patch  crmsd_patch
-abinitio::stage3a_patch crmsd_patch
-abinitio::stage3b_patch crmsd_patch
-abinitio::stage4_patch  crmsd_patch

where crmsd_patch is the name of the patch file

  1. Make sure the ab-initio flag file you are using provides the reference native structure with the flag -in::file::native