Re: [ccp4bb] dictionary for DNA in Coot/Refmac

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

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From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-10-23

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Subject: Re: dictionary for DNA in Coot/Refmac
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2007-10-23

Hi Sabine,

in addition to what Christian has written, please, also check whether
the ribose atom names contain a "*" instead of "'" to conform with
the PDB convention.

Best regards,

Dirk.

Am 22.10.2007 um 21:37 schrieb Christian Biertumpfel:

> Hi Sabine,
> Your problem might be an issue of the PDB format. I had troubles
> using a
> DNA model in coot which was refined in cns (3 letter code). When I
> converted it to the single letter notation everything was fine in
> coot/refmac.
>
> Tschüß,
> christian
>
>
>
> Sabine Schneider wrote:
>> Hi everyone,
>>
>> I am working on Protein-DNA complex and am struggling to generate a
>> dictionary with the right bonds/restraints for a the ds DNA of 15nt
>> length with 1nt overhang and a lesion. How do I link the nucleotides
>> together and set the right restraints in the bit with the lesion?
>> Tried
>> to read in a bit of DNA into library scatcher to get an idea what
>> I have
>> to do, but failed. Also couldn't find any example cif-files.
>>
>> Thanks for your help in advance!
>>
>> Sabine
>>
> ______________________________________________________________________
> _
>
> Dr. Christian Biertümpfel
> Laboratory of Molecular Biology
>
> NIDDK/National Institutes of Health phone: +1 301 402
> 4647
> 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496
> 0201
> Bethesda, MD 20892-0580
> USA
> ______________________________________________________________________
> _

*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
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81377 Munich
Germany
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Fax: +49-89-2180-76999
E-mail: kostrewa@lmb.uni-muenchen.de
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CCP4bb navigation

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

Previous message:
Subject: Re: Twinning
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-10-23

Next message:
Subject: Fw: Re: Twinning
From: Jorge Iulek iulek {- at -} INTERPONTA {- dot -} COM {- dot -} BR
Date: 2007-10-23