Does the Rebuild Tool depend on the initial state?
|Opened on:||Wednesday, December 26, 2018 - 09:24|
|Last modified:||Thursday, January 3, 2019 - 20:29|
Say you have a protein structure scoring 9000.000 and select its
residues 30-40 for rebuilding. After the 1st rebuild, you have a
score of 5800.000. At this point, what has a better chance of
giving you a good-scoring rebuild of residues 30-40: starting
from the structure with score 9000.000 or starting from the
structure with score 5800.000? Does rebuild only care about
the endpoints of residues 30-40, their sequence, and their
assigned secondary structure, which should be the same for
both scores 9000.000 and 5800.000, so both starting structures
should have the same chance of giving a structure with a score
of 9300.000 when residues 30-40 get rebuilt?
Also, does rebuild's results depend on the wiggle power or
clashing importance settings? What settings give the best
chance for a good-scoring rebuild?