[phenixbb] sugar puckering in DNA

chern chern at ualberta.ca
Fri Oct 24 09:43:44 PDT 2008

Sorry, I gave a wrong subject name in my previous e-mails. Should've been 
sugar puckering in DNA.
I am wondering why the default .cif file for DNA does not include all 
information about sugar puckers.
I do not have some fancy nucleotides. They are regular.


----- Original Message ----- 
From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
To: <phenixbb at phenix-online.org>
Sent: Friday, October 24, 2008 10:03 AM
Subject: Re: [phenixbb] elbow

>> The answer is yes but there may be better options.  Ralf is the best
>> person to answer this question but one option is to start with the .cif
>> file in the monomer library.
> This is more a chemistry question than a formatting question.
> Since I'm not deeply familiar with the DNA chemistry, I was pointing
> Maia to phenixbb in hopes that someone may already have figured out
> the list of torsion angle restraints to fix sugar puckers.
> What Maia really wants is:
>> could you please send me a specific example of how to modify a cif file
>> to specify the sugar puckers in DNA (I want them C2'-endo).
> Has anyone on this list done this already?
> Ralf
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