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Questions and answers => RNA structures (DSSR) => DSSR-NAR paper => Topic started by: xiangjun on July 07, 2015, 05:34:29 pm

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Title: Supplementary Figure 6 -- DSSR-identified k-turn in the SAM-I riboswitch
Post by: xiangjun on July 07, 2015, 05:34:29 pm

(http://x3dna.bio.columbia.edu/dssr-nar/supp-fig6-kturn-2gis/supp-fig6-kturn.png)

Quote

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.

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Starting from 2gis.pdb downloaded from the RCSB website, here is the complete script.

Code: Bash

1. x3dna-dssr -i=2gis.pdb -o=2gis.out --prefix=2gis
2. \cp 2gis-Kturns.pdb 2gis-kturn.pdb
3. x3dna-dssr -i=2gis-kturn.pdb -o=2gis-kturn.out --helical-axis
4. \cp dssr-helicalAxes.pdb 2gis-kturn-helices.pdb
5. x3dna-dssr -i=2gis-kturn.pdb -o=2gis-kturn-blocks.r3d --block-file
6.  
7. pymol -qkc 2gis-kturn.pml
8. 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)

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