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(http://x3dna.bio.columbia.edu/dssr-nar/supp-fig6-kturn-2gis/supp-fig6-kturn.png)
Figure S6: The k-turn identified by DSSR in the SAM-I riboswitch (PDB id: 2gis). Base-stacking interactions are interrupted around the k-turn even though the backbone is continuous along each strand. Thus DSSR assigns two helices (depicted by gray lines), the canonical helix on the left, and the noncanonical one on the right.
Starting from 2gis.pdb downloaded from the RCSB website, here is the complete script.
x3dna-dssr -i=2gis.pdb -o=2gis.out --prefix=2gis
\cp 2gis-Kturns.pdb 2gis-kturn.pdb
x3dna-dssr -i=2gis-kturn.pdb -o=2gis-kturn.out --helical-axis
\cp dssr-helicalAxes.pdb 2gis-kturn-helices.pdb
x3dna-dssr -i=2gis-kturn.pdb -o=2gis-kturn-blocks.r3d --block-file
pymol -qkc 2gis-kturn.pml
convert -trim +repage -border 10 -bordercolor white 2gis-kturn-pymol.png 2gis-kturn.png
Note:
- The --helical-axis option outputs the best-fitted helical axes in file "dssr-helicalAxes.pdb".
- The --block-file option creates a .r3d file with bases (or Watson-Crick base pairs) in rectangular block represention.
- The convert program is from ImageMagick that is used here to trim extra white boundaries.
- The png image was annotated using InkScape for the final illustration.
- For completeness, here is the tarball file containing all the data files and the script ("tasks"): supp-fig6-kturn-2gis.tar.gz (http://x3dna.bio.columbia.edu/dssr-nar/supp-fig6-kturn-2gis.tar.gz)
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