Pathway Gap Filling Post-CHECKSPMUTATE
Introduction
This is a recommended procedure to be used following the use of CHECKSPMUTATE, if it was a pathway which was being reoptimised.
CHECKSPMUTATE mutates a selected set of residues in a protein or protein+ligand system, and reoptimises all of the stationary points from the original system. Thus mutated forms or a close homologue can be directly compared against a wild type protein. This is particularly useful when comparing a particular protein fold or protein+cofactor interaction. In these instances, we are interested in reoptimising only the stationary points comprising a particular pathway, and the database before mutation is set up accordingly.
It is almost inevitable (particularly is we are introducing bulky mutations) that not all of the stationary points post-mutation will reoptimise (there could be steric clashes etc). Thus, there will be gaps in our new, mutated pathway. Hence the need for post-processing to fill these gaps.
Please note this method listed below is highly idiosyncratic, and as such is only meant as a loose guide. It uses very simple bash scripts, which can be easily edited. Please feel free to adapt the procedure to your own needs/preferences.
Method
The directories used for CHECKSPMUTATE and its post-processing. The bash scripts are set up to move between these, so will need to be adapted if the directories are named/organised differently.
Ordinarily, I will have run two CHECKSPMUTATE calculations in