[ccp4bb] model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: protein-protein docking programs
From: Jerry McCully for-crystallizaiton {- at -} HOTMAIL {- dot -} COM
Date: 2008-05-02

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From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-05-02

Subject: model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2008-05-02

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
refinement

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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: protein-protein docking programs
From: Jerry McCully for-crystallizaiton {- at -} HOTMAIL {- dot -} COM
Date: 2008-05-02

Next message:
Subject: sa omit map
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-05-02