refine, use potential modifications for full refinement

Syntax

The parameter can have the values yes or no.

Notes

1. No error message is generated when an uninterpretable value is entered for this parameter.
2. If no value is set, the default value is no.

Description

The first step in the refinement process is to model the selected sequences with the scoring, maximum missed cleavage parameter set to 5, the a list of list of potential modficiations defined by the refine, potential modification mass value. If this parameter is set to yes, then the new list of potential modifications are used in the subsequent steps of the refinement. If it is set to no, then the residue, potential modification mass value is used for the subsequent steps.