Dear Bob,
Date: Tue, 9 Dec 2008 18:20:58 -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
>
> make that
>
> then just
>
> > drawbox("box1", {-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.
> >
>
> oh -- I meant to add that I think these boxes are extremely cool. If
> they are at all simple to calculate, why don't we build them into
> Jmol?
>
Indeed they are very cool. The rectangular block representation was
initiated by Calladine-Drew in their classic DNA structure work (see:
Understanding DNA: the Molecule and How It Works). I implemented it firstly
in SCHNAaP/SCHNArP, and later in the 3DNA software package for schematic
visualization of nucleic acid structures, and I call them Calladine-Drew
style representations.
In addition to links mentioned in my previous post, please have a look at
(random pick):
http://ndbserver.rutgers.edu/atlas/xray/indexes/xray.dna.quad-1.html. They
are generated automatically by the 'blocview' script from 3DNA. I can help
more if you decide to add Jmol support for it.
Date: Tue, 9 Dec 2008 18:23:29 -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
>
> On Tue, Dec 9, 2008 at 10:02 AM, Xiang-Jun Lu <[EMAIL PROTECTED]> wrote:
> >
> > As far as Jmol's support for alchemy is concerned, I converted a sample
> PDB
> > file to alchemy using 'openbabel' and Jmol can read it without a problem.
>
> Can you send me that converted file? I'd like to see what Jmol is doing
> with it.
>
As an example, adenine in original PDB format:
http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/adenine.pdb
I used 'babel adenine.pdb adenine.alc' to get file adenine.alc:
http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/adenine.alc
The version of babel is: 'Open Babel 2.1.1 -- Mar 7 2008 -- 14:06:20'
The I rendered 'adenine.alc' in Jmol, as shown here:
http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/adenine_jmol_alc.png
Hope this classifies the issues.
Xiang-Jun
--
Xiang-Jun Lu (Ph. D.)
Creator & Maintainer of 3DNA
Email: [EMAIL PROTECTED]
http://3dna.rutgers.edu:8080/forum
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