3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: ghzheng on July 06, 2007, 11:10:46 am

Title: blocview base pairs
Post by: ghzheng 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.
Title:
Post by: xiangjun 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 (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/users.html). 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 (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?t=13) 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!

HTH,

Xiang-Jun