On Wed, Mar 12, 2014, Sidney Elmer wrote:
> This information was very helpful. I would like to build double
> stranded DNA with methylated cytosines directly in NAB using bdna().
> I looked through the NAB code and quickly got lost. I'm happy to do
> this myself, but I would appreciate some guidance as to how to do
> this. Could someone please outline the steps necessary to accomplish
> this? Thank you!
First, use NAB to build a standard BNDA helix [use fd_helix(), not bdna()].
See tutorial B1 for a detailed walk-through on how to do this.
An easier alternative for most cases is to visit w3dna.rutgers.edu.
Second, edit the PDB file to change the DC residue names to whatever your
library is calling methylated cytosine; let LEaP build the structure from
the un-methylated structure.
...good luck...dac
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Received on Wed Mar 12 2014 - 13:00:02 PDT
