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[ccp4bb] combine Se-SAD phase with Model-phase
 

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CCP4bb <-- 2008 <-- May 2008 <-- 07 May 2008
Previous message:
Subject: metal atoms written from coot in refmac
From: Leonard Thomas thomasle {- at -} ITS {- dot -} CALTECH {- dot -} EDU
Date: 2008-05-07 		Next message:
Subject: Re: combine Se-SAD phase with Model-phase
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-05-08


Subject: combine Se-SAD phase with Model-phase
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2008-05-07

Hi,
It would be of great help if you can give some
suggestion on the following problem.


I have two data sets of a
complex molecule. One is native (3.6A) and the other is Se-der
(4.5A). In one complex molecule I have one homo-dimer in complex with
DNA( 2 times 90 aa + 2 times 15 na = ~MW 28000, call it as component
1) plus a second long helical protein(130 aa, call it as component
2). I have two such complex molecule in the AU (space gr. P65).
I got a very good solution by
PHASER(using native data) for the component 1, but component 2 has
some ambiguity.
I used the solution of
component 1 and Se-der data to create Ano-diff Fourier map from model
phase. I got clear peaks at 3.5 sigma exactly at the Met-S positions.
I pulled out 11 Se sites, 9 of which are precisely exists at the
right positions looked upon the model component 1). Other 2 are
expecting on the two copy of component 2.
What I did next?
1. I used CNS to create both
SAD phase from Se and Model phase from component 1 and then combined
them. Used the combine HL co-eff to run density modification and
create 2Fo-Fc map. Very poor quality, but you can see some features.
2. Used only SAD phase from Se
sites and run density modification followed by 2Fo-Fc map
generation.
Useless map.
3. Run SHARP/AutoSHARP with Se
sites upto DM. Then run solvent flattening with model component 1.
No good map.
Do you know any other way to
go from here? Running rigid.inp, anneal.inp, minimize.inp and
bgroup.inp sequentially with the component 1 I reached R/R(free)
40%/45%.
Any suggestion is well
appreciated.
Regards...
Raja


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CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 07 May 2008
Previous message:
Subject: metal atoms written from coot in refmac
From: Leonard Thomas thomasle {- at -} ITS {- dot -} CALTECH {- dot -} EDU
Date: 2008-05-07 		Next message:
Subject: Re: combine Se-SAD phase with Model-phase
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-05-08


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