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$Id$
Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
What are all these files? Four of them are used by DnaGenerator.py
to create DNA structures in the CAD program:
adenine.mmp
cytosine.mmp
guanine.mmp
thymine.mmp
-----
3/29/2007
NOTE: I've since changed these four files by hand to add an oxygen to the 3'
carbon (where a bond point used to be), and removed the oxygen from the
phosphate (where a bond point is now.) This configuration is more standard in
the world of PDBs, GROMACS, and NAMOT, and is, in fact how the bdna.pdb file is
set up.
So the prepare.py script is out-of-date and will re-generate the old files if
run. Note that prepare.py is not typically run, but is documentation about how
the files where originally generated.
This change does make a chemical difference in that there should be an oxygen
bonded to the 3' carbon at the top of a 3'-to-5' strand (previously there was
not.) Technically, when the strands are generated, the oxygen should also be
hydrogenated *and* there should be no phosphate at the top of the 5'-to-3'
strand - but this change makes the nucleotides by themselves conform to
standards at least. A NAMOT-powered plugin should ultimately be used for the
generation of DNA.
--Brian.
-----
The other files are what I used to prepare these. I started with the
bdna.pdb file. I don't remember where I found it originally, but I
found another copy in these places, along with adna.pdb and zdna.pdb:
http://www.wellesley.edu/Chemistry/Flick/molecules/
http://chemistry.gsu.edu/glactone/PDB/DNA_RNA/
My hope is that bdna.pdb is an authoritative representation for what
DNA should really look like. I proceeded with that assumption.
-----
The first thing I did was load bdna.pdb and separate the two strands.
That gave me strand1.mmp and strand2.mmp.
Then I hand-edited the drawing styles for the atoms in strand1.mmp to
create strund1.mmp. The base pairs alternate between wireframe drawing
mode ("lin" in the MMP file) and default drawing mode ("def" in the
MMP file).
The prepare.py script parses strund1.mmp to extract the four base
pairs as MMP files. It tries to get bond orders and hybridizations
right, and it rotates and translates them to a standardized
orientation. The output of prepare.py is those first four files.
While working on Z-DNA, I used a slightly modified version of
prepare.py. It needed modification because Z-DNA's structure does a
zigzag on each pair of bonds.
------------------------
Here are some old notes, pertaining mostly to zdna.pdb
* http://en.wikipedia.org/wiki/DNA
* http://en.wikipedia.org/wiki/Image:Dna_pairing_aa.gif
The 5' and 3' terminators are respectively groups 32 (a single
hydrogen) and 359 (a hydroxyl). The groups representing base pairs are
as follows. The distances from the spinal carbon to the DNA axis
alternate for Z-DNA, so we'll need two copies of each base.
5' end (hydrogen)
1 cytosine 2.96
9 guanine 7.83
41 cytosine 2.97
74 adenine 7.79
104 adenine 2...
136 adenine 7...
168 thymine 2...
200 thymine 7...
232 thymine 2...
264 cytosine 7...
296 guanine 2...
326 cytosine 7...
3' end (hydroxyl)
The 5' and 3' ends are reversed for strand B. When a strand1 guanine
is viewed from the +Z direction, its oxygen points clockwise, where a
strand2 guanine's oxygen points counter-clockwise. That's what we
want, it means the same bases will work for both strands with
appropriate rotations. You get the strand2 version of the base by
rotating it 180 degrees about a radial vector, so that its 5' and 3'
connectors are reversed. Where the strand1 sequence is CGCAAATTTCGC,
the strand2 sequence is GCGTTTAAAGCG.
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