Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Author Topic: blocview base pairs  (Read 9134 times)

Offline ghzheng

  • with-posts
  • *
  • Posts: 23
    • View Profile
blocview base pairs
« on: July 06, 2007, 11:10:46 am »
blocview can be used to represent each base of DNA as a slabe. I have a normal double-helix B-DNA. Then is it possible to represent each BASE-PAIR as a slabe, rather than each base as a slabe?

What function should I use? and how? Thanks.

Offline xiangjun

  • Administrator
  • with-posts
  • *****
  • Posts: 1642
    • View Profile
    • 3DNA homepage
(No subject)
« Reply #1 on: July 08, 2007, 10:51:31 am »
Good question!

The utility "blocview" was designed to generates a schematic image which combines base block representation with protein ribbon. The image has informative color coding for the nucleic acid part and is set in the "best-view" by default.

For the nucleic acid part, the "primary" object is the planar base rings which are simplified by corresponding rectangular blocks. Base-pairs are only secondary objects, abstracted at a higher level. Moreover, except for normal Watson-Crick base-pairs, there is an issue of how to represent the "faces" of a pair. Also, think of triplets and higher order base associations. Those are the rationales that "blocview" generates only a block representation for each individual base.

I did have the bp block issue in mind when I wrote 3DNA, and it is possible to generate bp blocks for normal Watson-Crick base-pairs with 3DNA v1.5. Using bdl084 as an example, try the following steps:

Code: [Select]
   blocview bdl084.pdb
    cp t.pdb bdl084_bv.pdb
    find_pair bdl084_bv.pdb stdout | analyze

    frame_mol -s ref_frames.dat bdl084_bv.alc

    alc2img -r -n bdl084_bv.alc bdl084_bp.r3d
    cat t.r3d bdl084_bp.r3d > bdl084_all.r3d
    render < bdl084_all.r3d > bdl084.avs

    convert -trim +repage -border 5 -bordercolor white bdl084.avs bdl084.jpg

The generated image is attached below. Knowing what you are doing and taking 3DNA as a toolkit, you should be able to get what you want in a script. A possible simple starting point is by modifying the "blocview" Perl script. You might want to have a try and possibly contribute back once you are happy with your script. Do not forget that there is a Users' Corner section in 3DNA homepage. With enough interest,  I might consider to add a new script in 3DNA v2.0

As a side note, the ".r3d" file "bdl084_all.r3d" can be fed into Pymol directly to generate photo-realistic quality images. Please also refer to another post in this forum for further example images. Of course, you might be aware that "blocview" generated images are used in the NDB, and as a nice surprise (to me), now also  used in the PDB!




Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.