[phenixbb] sugar puckering in DNA

Hi Yu Seon. I would appreciate it very much if you send me your added restraints to the cif file. Maia YS. Chung wrote:

Hi Maia, I had the same problem when I was refining with phenix. I ended up looking at the torsions that were used in 3DNA (the program I used to analyze the puckerings) and manually added the restraints to the .cif files used in phenix. I can send you an example if you'd like. The puckerings improved a lot when I used the modified .cif files. Yu Seon

On Fri, 24 Oct 2008 10:43:44 -0600 "chern" wrote:

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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.

Maia

----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" To: Sent: Friday, October 24, 2008 10:03 AM Subject: Re: [phenixbb] elbow

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The answer is yes but there may be better options. Ralf is the

best

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person to answer this question but one option is to start with the

.cif

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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

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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:

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could you please send me a specific example of how to modify a cif

file

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to specify the sugar puckers in DNA (I want them C2'-endo).

Has anyone on this list done this already?

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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