Hi Xun, i'm not sure if i have the best way of doing it, but i've used a
cif dictionary file that contains base pair restraints for AT/GC base
pairs (sometimes with, sometimes without planar restraints depending on
the resolution), and then edit the PDB file header to contain LINKR
records that define each individual base pair in the structure. I can
send you examples if you like.
Alan
On 29/01/2010 06:14, Xun Lu wrote:
Dear all,
I am dealing with a protein/DNA complex. After restrained
refinement in Refmac, the bases have been brought closer to each other
(about 2A instead of 3A for H-bonding). But in our model, the geometry
of the DNA is fine (I even replaced my DNA with theirs by superimposing
and editing pdb file. The DNA sequence is almost the same: one base-pair
difference in a total 15 bps.)
So, how can I tell Refmac not to sacrifice the geometry of DNA
to fit my poor density? Or, how to fix the DNA (just like in CNS)?
Anyone could share their experience and tricks about dealing with DNA?
cheers
Xun
--
Department of Molecular and Structural Biochemistry
North Carolina State University
--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: che...@lmb.uni-muenchen.de
