Dear Nigel, I am sending you an ideal double-stranded B-DNA that I made in coot, but I was puzzled that it had C3*-exo puckers instead of C2*-endo. Probably they are equivalent. Anyway, if you can generate cif for me, I would appreciate it. Maia Nigel W Moriarty wrote:
Maia
If you have an example geometry of the C2'-endo eLBOW can generate the restraints. I'm happy to generate them for you if you have one. I'm provide a detailed procedure to list after.
Nigel
On 10/24/08 9:03 AM, Ralf W. Grosse-Kunstleve wrote:
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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