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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.
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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:
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
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University