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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