ROSIE docking2 and symmetric_docking runs both give plots
and spreadsheets containing many columns of data.
Which spreadsheet columns best reflect the quality of a run?
Should the best runs have each plot with a narrow funnel on the left
and a rather wide flat plateau to the right?
Should there be very few points scattered above or below the plateau?
If the plots don't look ideal, how can one improve them?
For docking2 runs (I have been using the local_docking protocol),
I have been trying to improve the plots by taking the best pdb file
from a run, inserting a TER line between the 2 parts I want to dock,
and using the resulting pdb file as an input for a new docking2
(local_docking) run. Is this the best way to proceed? What would
you do instead? Is it better to use the pdb file with the lowest score
or the lowest I_sc value as the initial condition for the next run?
If there is no clear funnel, which pdb file would you pick as the
initial condition for the next run? How will I know when no more
improvement will occur? How will I know when the funnel is as
deep as it can go?
What would you do to improve the results of a symmetric_docking run?
For example, will it let you input an entire symmetric multi-subunit complex
as its initial condition?