Before I write this reader, can I ask if it's possible you could use
another format?
Do you have all these files already made, so you are eager to use them
exactly, or do you have a program that produces them?
Because if it's a program that produces them, I suggest doing a little
modification to that program to produce Jmol scripts instead. That
would be far more efficient, and it should be pretty easy to make them
- probably just one small subroutine. Then you could do all sorts of
interesting things in relation to dynamically changing them,
displaying them, measuring them, etc., within Jmol. For example, that
one you show as a demo could be something like this:
pt1={-2.2500 5.0000 0.2500}
pt2={-2.2500 -5.0000 0.2500}
pt3={-2.2500 -5.0000 -0.2500}
pt4={-2.2500 5.0000 -0.2500}
pt5={2.2500 5.0000 0.2500}
pt6={2.2500 -5.0000 0.2500}
pt7={2.2500 -5.0000 -0.2500}
pt8={2.2500 5.0000 -0.2500}
draw box line @pt1 @pt2 @pt3 @pt4 @pt1 @pt5 @pt6 @pt7 @pt8 @pt5
draw side1 plane @pt1 @pt2 @pt3 @pt4
(not complete, but you get the idea)
But even better, you could define a Jmol function that draws the boxes
for you give the eight points:
function drawbox(name, pt1, pt2, pt3, pt4, pt5, pt6, pt7, pt8)
draw ID @{name + "_box"} line @pt1 @pt2 @pt3 @pt4 @pt1 @pt5 @pt6
@pt7 @pt8 @pt5
draw ID @{name + "_side1"} plane @pt1 @pt2 @pt3 @pt4
etc.
end function
then just
drawbox({-2.2500 5.0000 0.2500},{-2.2500 -5.0000 0.2500}
,{-2.2500 -5.0000 -0.2500} ,\
{-2.2500 5.0000 -0.2500},{2.2500 5.0000 0.2500},{2.2500
-5.0000 0.2500},\
{2.2500 -5.0000 -0.2500},{2.2500 5.0000 -0.2500})
for each box. It seems to me, for that matter, you only need three
points to define the box. So that would be even easier.
Now, if you are really fancy, what you do is embed those commands in
the pdb files themselves, so when the pdb file is loaded, the boxes
are all drawn automatically. Rolf can show you how he does that at
Jena.
And, better, if you are doing this based on some simple criterion in
PDB files, then you should be able to define a function that allows
drawing of such boxes for the entire model all within Jmol. That would
be REALLY COOL, because then anyone could do it with any PDB file. I
have such a function (somewhere), for example, for drawing all the
peptide planes.
Bob
On Sun, Dec 7, 2008 at 5:24 PM, Xiang-Jun Lu <[EMAIL PROTECTED]> wrote:
> Hi,
>
> Over the years, I have been using RasMol 2.6.4 (from Roger Sayle) for
> interactive rendering of a 3DNA-specific rectangular schematic
> representation of base and base-pair geometry. As an example image, please
> see:
> http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp-rasmol2-6-4.png
>
> Recently, I am considering to use Jmol as well, given the great support of
> the Jmol community (as is evident from this list). While Jmol recognizes a
> regular alchemy format file without a problem, it does not render my
> schematic alchemy file as expected (e.g.,
> http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp.alc): a sample image
> is shown at: http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp-jmol.png
>
> Essentially, I am playing tricks with the alchemy format purely as a
> rendering tool by specifying explicitly each node and linkage, no chemistry
> at all. Hopefully, Jmol would be able to render it as well, just as RasMol
> does.
>
> Thanks,
>
> Xiang-Jun
>
> --
> Xiang-Jun Lu (Ph. D.)
> Creator & Maintainer of 3DNA
> Email: [EMAIL PROTECTED]
> http://3dna.rutgers.edu:8080/forum
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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