Henry, I've devised a (very) dirty solution:
duplicate residue 1 as nr. 9
The trace or cartoon is very sharp at the connection, so things get
better if we shift the residue numbering, such as making
1 -> 6
2 -> 7
3 -> 8
4 -> 1
5 -> 2
6 -> 3
7 -> 4
8 -> 5
9 is a copy of the new residue 1 (former 6
>Hi Henry
>Nice molecule!
It (sort of ) has D2 symmetry, and is therefore dissymetric in its own right
> I had only known cyclic DNA molecules as in
>"circular" DNA, e.g. procariotic DNA and plasmids. Chemicaly there is
>not much difference.
>Just for info, RasMol and Accelrys DS Visualizer don
Well, it is not based on residue numbering.
A possible way to deal with this ould be to parse the pdb information
in LINK records.
Henry's file (2HK4.pdb) has them:
LINK P C A 1 O3* T A 8
LINK P C B 1 O3* T B 8
the bonds are there; it's just the cartoons that are not.
On Wed, Jan 28, 2009 at 5:16 AM, Rzepa, Henry wrote:
> Quick follow up to http://www.ch.ic.ac.uk/local/organic/pericyclic/2HK4.html
>
> Kinemage (which is more veritable than Jmol), also fails to close the cycle
> on cyclic DNA, so I
Hi Henry
Nice molecule! I had only known cyclic DNA molecules as in
"circular" DNA, e.g. procariotic DNA and plasmids. Chemicaly there is
not much difference.
I don't know the exact code being used fior calculating and rendering
cartoons et al., but I guess it is based on phosphorus IDs and
r
Quick follow up to http://www.ch.ic.ac.uk/local/organic/pericyclic/2HK4.html
Kinemage (which is more veritable than Jmol), also fails to close the cycle
on cyclic DNA, so I presume that Jmol is merely following the convention in
this regard in how it also does this.
I guess this is a bit o
I am interested in the properties of a class of DNA called cyclic DNA. An
example can be seen at
http://www.ch.ic.ac.uk/local/organic/pericyclic/2HK4.html
This consists of two loops of cyclic 8-mers of DNA bound by Watson-Crick
pairing. The two separate monomers, when displayed as ball and
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