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Questions and answers => RNA structures (DSSR) => DSSR-NAR paper => Topic started by: xiangjun on July 05, 2015, 08:55:54 am

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Title: Supplementary Figure 1 -- four base triplets in yeast phenylalanine tRNA (1ehz)
Post by: xiangjun on July 05, 2015, 08:55:54 am

(http://x3dna.bio.columbia.edu/dssr-nar/supp-fig1-1ehz-multiplets/1ehz-multiplets.png)

Quote

Figure S1: The four base triplets and associated hydrogen bonds (dashed lines) detected by DSSR in yeast tRNA^Phe (PDB id: 1ehz). (A) UAA (U8,A14,A21), with a reverse Hoogsteen U8–A14 pair. (B) AUA (A9,U12,A23). (C) gCG (2MG10,C25,G45). (D) CGg (C13,G22,7MG46). Here, the bases in each triplet are listed in sequential order, with the one-letter shorthand form followed by more detailed identifiers in parentheses. In (C) and (D), the lower case ‘g’ represents the shortened name for modified guanine nucleotides 2MG10 and 7MG46, respectively. Note that the triplets and hydrogen bonds match those originally reported by Quigley and Rich for yeast tRNA^Phe.

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Starting from "1ehz.pdb" downloaded from RCSB PDB, here is the complete script to get each of the four base-triplet images in png format.

Code: Bash

1. x3dna-dssr -i=1ehz.pdb -o=1ehz.out --prefix=1ehz
2.  
3. ex_str -1 1ehz-multiplets.pdb 1ehz-m1.pdb
4. x3dna-dssr -i=1ehz-m1.pdb -o=1ehz-m1.pml --hbfile-pymol
5. pymol -qkc 1ehz-m1.pml
6. convert -trim +repage -border 10 -bordercolor white 1ehz-m1-pymol.png 1ehz-m1.png
7.  
8. ex_str -2 1ehz-multiplets.pdb 1ehz-m2.pdb
9. x3dna-dssr -i=1ehz-m2.pdb -o=1ehz-m2.pml --hbfile-pymol
10. pymol -qkc 1ehz-m2.pml
11. convert -trim +repage -border 10 -bordercolor white 1ehz-m2-pymol.png 1ehz-m2.png
12.  
13. ex_str -3 1ehz-multiplets.pdb 1ehz-m3.pdb
14. x3dna-dssr -i=1ehz-m3.pdb -o=1ehz-m3.pml --hbfile-pymol
15. pymol -qkc 1ehz-m3.pml
16. convert -trim +repage -border 10 -bordercolor white 1ehz-m3-pymol.png 1ehz-m3.png
17.  
18. ex_str -4 1ehz-multiplets.pdb 1ehz-m4.pdb
19. x3dna-dssr -i=1ehz-m4.pdb -o=1ehz-m4.pml --hbfile-pymol
20. pymol -qkc 1ehz-m4.pml
21. convert -trim +repage -border 10 -bordercolor white 1ehz-m4-pymol.png 1ehz-m4.png

Note:

• The --prefix option makes the auxiliary files having a specified prefix instead of the default "dssr". For example, "dssr-multiplets.pdb" becomes "1ehz-multiplets.pdb".
• The ex_str utility program is from the 3DNA distribution. It is used to extract a specific model from a MODEL/ENDMDL ensemble.
• The DSSR --hbfile-pymol option is used to generate a .pml file with all required settings for rendering in PyMOL.
• The convert  program is from ImageMagick that is used here to trim extra white boundaries.
• The multiplet-png images (here four triplets) were combined using InkScape, and annotated, to get the final illustration.
• For completeness, here is the tarball file containing all the data files and the script ("tasks"): supp-fig1-1ehz-multiplets.tar.gz (http://x3dna.bio.columbia.edu/dssr-nar/supp-fig1-1ehz-multiplets.tar.gz)

Here is a sample image generated with the above script:

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(http://x3dna.bio.columbia.edu/dssr-nar/supp-fig1-1ehz-multiplets/1ehz-m1.png)

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.