Re: [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: Refining against images instead of only reflections
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2010-01-29

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Subject: Re: Very high B-factors of some atoms of ligand in Refmac
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-01-29

Subject: Re: how to deal with the DNA in Refmac?
From: Alan Cheung cheung {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2010-01-29

Hi Xun, i'm not sure if i have the best way of doing it, but i've used a
cif dictionary file that contains base pair restraints for AT/GC base
pairs (sometimes with, sometimes without planar restraints depending on
the resolution), and then edit the PDB file header to contain LINKR
records that define each individual base pair in the structure. I can
send you examples if you like.

Alan

On 29/01/2010 06:14, Xun Lu wrote:
> 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

--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: cheung@lmb.uni-muenchen.de

CCP4bb navigation

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

Previous message:
Subject: Re: Refining against images instead of only reflections
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2010-01-29

Next message:
Subject: Re: Very high B-factors of some atoms of ligand in Refmac
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-01-29