Thanks to Rolf and Angel for their quick and details responses  -- I am
subscribing in digest-mode, and thus can't get back promptly with reach

Let me explain in more details using base-pair rectangular schematic
representation the way it is and some of its advantages/applications.

   - Firstly, I adopted the alchemy format in 3DNA primarily because it is
   one of the formats supported by RasMol. PDB format is also used in 3DNA for
   atomic representations, and the alchemy format is simpler for schematics by
   specifying each node/linkage explicitly.
   - As I mentioned in my previous message, I am "playing tricks" with the
   alchemy format by overlapping nodes to get minor-groove information. The 4
   nitrogen atoms (1 to 4) are in exact the same positions as the last four
   carbon atoms 9-12. However, the linkage information on the minor groove side
   uses only the 4 Ns, and the last four Cs are only connected with 5-8. Thus
   when rendered in RasMol, the minor groove side is blue and the other parts
   are white.
   - 3DNA provides a utility program, 'alc2img', to convert the alchemy
   format into EPS and Xfig format, as shown in the 3DNA example page: More example can
   be seen in
   - 3DNA also has a utility program, 'blocview', which generates schematic
   image (showing the minor groove info clearly) in the most extended view (by
   default). Program 'blocview' is a Perl script, which internally calls
   MolScript and Render (also PyMol) to generate representations of protein and
   nucleic acid backbone. Simple as it is, all NDB images and the static
   nucleic acid containing images in the PDB are created with 'blocview'.

In relation to Jmol, I am hoping Jmol could render such
"non-chemistry-based" alchemy file properly. In essence, the render just
needs to respect the node and linkage information explicitly defined in the
file: it does not try to be "clever" to deduce some chemistry from it.

Best regards,


Xiang-Jun Lu (Ph. D.)
Creator & Maintainer of 3DNA
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