[ccp4bb] how to deal with the DNA in Refmac?

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

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Subject: Re: What is an aceptable spread in ADP values?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-01-28

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From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-01-29

Subject: how to deal with the DNA in Refmac?
From: Xun Lu xluncsu {- at -} GMAIL {- dot -} COM
Date: 2010-01-28

Dear all,

I am dealing with a protein/DNA complex. After restrained refinement
in Refmac, the bases have been brought closer to each other (about 2A
instead of 3A for H-bonding). But in our model, the geometry of the DNA is
fine (I even replaced my DNA with theirs by superimposing and editing pdb
file. The DNA sequence is almost the same: one base-pair difference in a
total 15 bps.)

So, how can I tell Refmac not to sacrifice the geometry of DNA to
fit my poor density? Or, how to fix the DNA (just like in CNS)? Anyone could
share their experience and tricks about dealing with DNA?

cheers

Xun

--
Department of Molecular and Structural Biochemistry
North Carolina State University

CCP4bb navigation

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

Previous message:
Subject: Re: What is an aceptable spread in ADP values?
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-01-28