Does the Rebuild Tool depend on the initial state?

Case number:845813-2006342
Topic:Game: Tools
Opened by:jeff101
Status:Open
Type:Question
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?

Thanks!
Jeff

(Wed, 12/26/2018 - 09:24  |  1 comment)


bkoep's picture
User offline. Last seen 4 days 5 hours ago. Offline
Joined: 11/15/2012
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No, the structures returned by Rebuild do not depend on the initial score. The Rebuild algorithm only depends on the endpoints of the selection, their sequence, and assigned secondary structure.

I don't believe wiggle power or clashing importance will have any impact on the structures returned by Rebuild.

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