Analysis  |  Rebuilding  |  Visualization

Analysis   [Back to Top]

Using a high-resolution B-DNA dodecamer, bdl084 (Shui et al. (1998), Biochemistry, 37, 8341-8355), as an example, the input and output files for the analysis program (analyze) are as follows:

1. Input
   • bdl084.pdb: structure file in PDB format downloaded from the NDB/PDB
   • bdl084.inp: input file describing base-pairing patterns in the original PDB file, generated as follows: find_pair bdl084.pdb bdl084.inp
2. Output (generated with: analyze bdl084.inp)
   • bdl084.out: detailed listing of various parameters
   • auxiliary.par: auxiliary parameters including phosphorus-phosphorus distance matrix, etc. Fixed file name: overwritten each time unless changed to a new name
   • bp_helical.par: base-pair and helical parameters (x-displacement, etc.) in a format suitable for rebuilding routines (e.g., rebuild)
   • bp_step.par: base-pair and step parameters (Roll, Slide etc.) in a format suitable for rebuilding routines
   • cf_7methods.par: parameters of the seven most frequently used nucleic acid analysis programs-CEHS, CompDNA, Curves, FreeHelix, NGEOM, NUPARM, RNA-calculated based on the standard reference frame. Note that the numerical values are very similar
   • ref_frames.dat: position and orientation of each base-pair reference frame, useful for re-orienting the structure with frame_mol
   • poc_haxis.r3d: global linear helical axis with average radii of P, O4' and C1' atoms for input to Raster3D.
   • hstacking.pdb: multiple structures in PDB format composed of each dinucleotide step with reference to its middle helical frame
   • stacking.pdb: multiple structures in PDB format composed of each dinucleotide step with reference to its middle step frame. Used for generating "standardized" stacking diagrams

Rebuilding   [Back to Top]

With 3DNA, nucleic acid structures can be generated based on base-pair step and helical parameters as generated by analyze shown above, arbitrary user-defined parameter sets, or regular fiber models.

1. Rebuild based on structural parameters
   • Illustration of base-pair parameters (download this image in PostScript format)

     

   • A complete helical turn of DNA having Twist = 36°, showing the effects of introducing uniform Roll and Slide at each step. [Calladine & Drew (1997), "Understanding DNA: The Molecule and How It Works", 2nd Edition, pp56.]

     

   • Two complete helical turns of DNA, with a curvature of 45° per turn, or 4.5° per step on average. Such tight curvature may be achieved, in principle, by any of the distributions of Roll angle shown in parts (a) to (d). [Calladine & Drew (1997), "Understanding DNA: The Molecule and How It Works", 2nd Edition, pp78.]

     

2. Fiber models: 55 fiber models can be conveniently generated with the program fiber.

Visualization   [Back to Top]

• Stacking diagrams: based on the file stacking.pdb generated with analyze shown above, the following image can be produced directly with stack2img and rendered with Raster3D.

  

• Base multiplets can be automatically identified and oriented in the best view with the utility program find_pair. The following image was generated with r3d_atom and rendered with Raster3D.

  

• Double helical regions are automatically identified by find_pair, and relatively straight helices can be rendered as cylinders, as shown in the following example of a nucleic acid junction (Nowakowski et al. (2000) J Mol Biol., 300(1), 93-102).

  

• The schematic output from 3DNA progams, such as stack2img, r3d_atom and blocview, can also be fed directly to PyMol to get high-quality ray-traced images, as shown in the following examples: