I'll set it up tonight
On Dec 9, 2008, at 7:21 PM, "Xiang-Jun Lu" <[EMAIL PROTECTED]> wrote:
Dear Bob,
Thank you so much for your detailed explanations.
Date: Tue, 9 Dec 2008 18:19:09 -0600
From: "Robert Hanson" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
schematic base-pair geometry
To: jmol-users@lists.sourceforge.net
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Before I write this reader, can I ask if it's possible you could use
another format?
I could, but I really do not have a solid reason to (see below).
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?
Yes, I have several (utility) programs within 3DNA that produce and
read such alchemy files for various (internal) purposes. It is nice
that RasMol can render them properly, but essentially, 3DNA is a
suite of command-line driven programs which do not rely on RasMol
for using the alchemy files.
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
Given the amazing support of Jmol from you and others, I have been
considering to use Jmol (and eventually switch to it), and then came
cross the alchemy format issue. All the cool stuffs you mentioned
are very impressive, and I will surely dig more deeply into Jmol in
the future. However, I still think a simple render of the alchemy
format in Jmol would be ideal. Then people like me could simply load
the alchemy file into Jmol to visualize it without writing any Jmol-
specific scripts.
I have checked RasMol v2.6.4 source code, and found the alchemy
reader is via function LoadAlchemyMolecule() in infile.c, and it is
pretty short. The data directory even has an example file
'asprin.alc'.
Since there is no official alchemy document, and given the problem
that 'openbabel' has with my non-chemistry oriented alchemy file
(see my previous post), maybe one could forget the complexity of
atom/bond types, just take them as nodes and linkages, and Jmol
would render the file at face value.
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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