Re: [ccp4bb] How to run SIGMAA twice in a row? (fwd)

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CCP4bb <-- 2007 <-- April 2007 <-- 20 April 2007

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Subject: Re: GUI problem with SIGMAA
From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2007-04-20

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Subject: Re: How to run SIGMAA twice in a row? (fwd)
From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2007-04-20

Hi Pete,

The sigmaa-weighing scheme implemented in SigmaA routine is the very means
to remove the potential model bias. Also, the model phases we used in the
phase combination were simply from a backbone poly-Ala model generated
from the best parts of the MAD-phased density (some of them from an
ARP/wARP run) leaving out the surface regions where the map quality is
marginal. Combining partial model phases with the experimental phases has
been used as a way to improve the map quality while the partial model is
still far from complete and most of the side chains are not yet filled
in. Once enough scattering mass has been built into the model and a
reciprocal space refinement with CNS or REFMAC is warranted, the
resulting 2Fo-Fc and Fo-Fc maps are often having much suprior quality for
the further model building.

One drawback of combining partial model phases with the density-modified
experimental phases is that one cannot run the density modification second
time after the combination. I have not tested whether combining model
phases with the density modified MAD phases produces good quality map
(experts in the field can make comments). I did get significant
improvement in the map quality with the combine-then-modify procedure.

HTH,

Huiying

On Fri, 20 Apr 2007, Peter Adrian Meyer wrote:

>> structure" running mode of SIGMAA. This is the run we really wanted to
> combine
>> the model phases with the MAD phases before going through further
> density
>> modifications with SOLOMON or DM.
>
> I would have thought that you'd want to do this the other way around
> (density modification on MAD before model phase combination) in order to
> reduce possible model bias.
>
> I'm curious...what's the reasoning for doing the model phase combination
> first?
>
> Pete
>
>
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>
>
>
>

--
-------------------------------------------------
Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953); Fax: 949-824-3280
email: hli@uci.edu
--------------------------------------------------

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CCP4bb <-- 2007 <-- April 2007 <-- 20 April 2007

Previous message:
Subject: Re: GUI problem with SIGMAA
From: Huiying Li hli {- at -} CRYSTAL {- dot -} BIO {- dot -} UCI {- dot -} EDU
Date: 2007-04-20

Next message:
Subject: Ecoli protein staining with AntiHis?
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2007-04-20