RNA cartoon-block representations with PyMOL and DSSR

[xiangjun]

In addition to its functionality for RNA structural analysis, the DSSR program also introduces novel cartoon-block schematic representations of nucleic acid structures to be rendered with PyMOL. Illustrated below are four sample images with the script and all data files (cartoon-block.tar.gz).

Here is the script (named tasks in the associated tarball cartoon-block.tar.gz):

Code: Bash

1. # ------------------------------------------------------------------
2. # 1. Yeast phenylalanine tRNA 1ehz in default settings.
3.  
4. # Note the coordinates ("1ehz-ok.pdb") is transformed from the
5. # original PDB file "1ehz.pdb" to put the helix containing the T-stem
6. # and acceptor stem horizontally, and the helix containing the D-stem
7. # and anti-codon stem 'vertically'.
8.  
9. x3dna-dssr -i=1ehz-ok.pdb --helical-axis -o=temp  # note the --helical-axis option
10. \mv dssr-helicalAxes.pdb 1ehz-ok-helices.pdb       # rename file with helical axes
11. x3dna-dssr -i=1ehz-ok.pdb --block-file -o=1ehz-ok-blocks.r3d  # note the option --block-file
12.  
13. # The three files "1ehz-ok.pdb", "1ehz-ok-blocks.r3d", and
14. # "1ehz-ok-helices.pdb" combined in "1ehz-ok.pml" and ray-traced with
15. # PyMOL to get "1ehz-ok-pymol.png".
16.  
17. pymol -qkc 1ehz-ok.pml
18. convert -trim +repage -border 10 -bordercolor white 1ehz-ok-pymol.png 1ehz-ok.png # just to crop
19.  
20. # ------------------------------------------------------------------
21. # 2. tRNA 1ehz with thicker rectangular blocks and Watson-Crick bps in
22. #    longer blocks.
23.  
24. \cp 1ehz-ok.pdb 1ehz-wc.pdb  # just give it a different name
25. x3dna-dssr -i=1ehz-wc.pdb --helical-axis -o=temp
26. \mv dssr-helicalAxes.pdb 1ehz-wc-helices.pdb
27. x3dna-dssr -i=1ehz-wc.pdb --block-file=wc --block-depth=1.2 -o=1ehz-wc-blocks.r3d
28.  
29. # Note the options "--block-file=wc" and "--block-depth=1.2". The
30. # default block thickness (depth) is 0.5 angstrom. Again, file
31. # "1ehz-wc.pml" combines the components to be ray-traced by PyMOL.
32.  
33. pymol -qkc 1ehz-wc.pml
34. convert -trim +repage -border 10 -bordercolor white 1ehz-wc-pymol.png 1ehz-wc.png
35.  
36. # ------------------------------------------------------------------
37. # 3. GUAA tetraloop mutant of sarcin/ricin domain from E. Coli 23S
38. #    rRNA -- 1msy, with minor groove in black and oriented in a bp
39. #    reference frame.
40.  
41. x3dna-dssr -i=1msy.pdb --frame=A.2658+edge+wc -o=1msy-ok.pdb # set the view
42. x3dna-dssr -i=1msy-ok.pdb -o=temp
43. x3dna-dssr -i=1msy-ok.pdb --block-file=minor+wc --block-depth=0.8 -o=1msy-ok-blocks.r3d
44.  
45. # Note the options "--frame=A.2658+edge+wc" and
46. #                  "--block-file=minor+wc".
47. # The "1msy-ok.pml" file is for PyMOL rendering.
48.  
49. pymol -qkc 1msy-ok.pml
50. convert -trim +repage -border 10 -bordercolor white 1msy-ok-pymol.png 1msy-ok.png
51.  
52. # ------------------------------------------------------------------
53. # 4. 1msy, with blocks in outline mode.
54.  
55. \cp 1msy-ok.pdb 1msy-edge.pdb
56. x3dna-dssr -i=1msy-edge.pdb -o=temp
57. x3dna-dssr -i=1msy-edge.pdb --block-file=edge -o=1msy-edge-blocks.r3d
58.  
59. # Note the option "--block-file=edge", and file "1msy-edge.pml".
60.  
61. pymol -qkc 1msy-edge.pml
62. convert -trim +repage -border 10 -bordercolor white 1msy-edge-pymol.png 1msy-edge.png

Following the above instructions, one should be able to reproduce the four sample images without a problem. Similar procedures can be easily applied to any other nucleic acid structures. Hopefully, this schematic visualization feature provides yet another reason for you to give DSSR a try.

Thomas Holder, the Principal Developer of PyMOL, has written a PyMOL plugin that implements the dssr_block command. Now users can create "block" shaped cartoons for nucleic acid bases and base pairs interactively in PyMOL.

Note added on 2016-04-01: DSSR now also has two new related options, --cartoon-block and --block-color, to make the generation of schematic cartoon block images more straightforward, and flexible.