[phenixbb] model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch

hari jayaram harijay at gmail.com
Fri May 2 08:47:28 PDT 2008

First off sorry for the cross post across bbs

I have a molecular replacement solution for a single site mutant for data
that goes out to 2.8 A.
After molecular replacement in phaser I run the following and examine the
maps for bias from the model.

Option1: simluated annealing refinement in phenix using the phaser mtz

Option2: take the phaser mtz and then just run prime and switch in resolve
and look at the map

Option3: First part: take the phaser mtz and then run simulated annealing
and sigmaa in cns 1.2.2 . Second part: Run prime-and-switch using part1s
model phases and modified Fs

I am observing that Option 1 and Option 2 the maps are indistinguishable
from each other and show very little bias from the model.
In Option 3 just cns simulated annealing does not go as far at removing bias
as cns simulated annealing plus prime-and-switch.

Although my estimate of model bias is just a "look and see" feeling. Since I
lack a thorough understanding of the relative merits of these algorithms
I have the following questions

1)Does simulated annealing refinement as implemented in phenix use a
prime-and-switch style approach to modify phases at any point to guide the

2) Am I wrong in assuming that just simulated annealing and sigma-aa
weighted maps for cns (Option 3 part 1) are not as good as  cns simulated
annealing + sigmaa+ prime_and_switch ( option3 part 2)

Hoping to get a better idea on how well these approaches fair at removing
model bias

Hari Jayaram
Postdoc , Brandeis University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20080502/ebc4dda8/attachment-0003.htm>

More information about the phenixbb mailing list