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RNA cartoon-block representations with PyMOL and DSSR
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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. Yeast phenylalanine tRNA 1ehz in default settings. # Note the coordinates ("1ehz-ok.pdb") is transformed from the# original PDB file "1ehz.pdb" to put the helix containing the T-stem# and acceptor stem horizontally, and the helix containing the D-stem# and anti-codon stem 'vertically'. x3dna-dssr -i=1ehz-ok.pdb --helical-axis -o=temp # note the --helical-axis option\mv dssr-helicalAxes.pdb 1ehz-ok-helices.pdb # rename file with helical axesx3dna-dssr -i=1ehz-ok.pdb --block-file -o=1ehz-ok-blocks.r3d # note the option --block-file # The three files "1ehz-ok.pdb", "1ehz-ok-blocks.r3d", and# "1ehz-ok-helices.pdb" combined in "1ehz-ok.pml" and ray-traced with# PyMOL to get "1ehz-ok-pymol.png". pymol -qkc 1ehz-ok.pmlconvert -trim +repage -border 10 -bordercolor white 1ehz-ok-pymol.png 1ehz-ok.png # just to crop # ------------------------------------------------------------------# 2. tRNA 1ehz with thicker rectangular blocks and Watson-Crick bps in# longer blocks. \cp 1ehz-ok.pdb 1ehz-wc.pdb # just give it a different namex3dna-dssr -i=1ehz-wc.pdb --helical-axis -o=temp\mv dssr-helicalAxes.pdb 1ehz-wc-helices.pdbx3dna-dssr -i=1ehz-wc.pdb --block-file=wc --block-depth=1.2 -o=1ehz-wc-blocks.r3d # Note the options "--block-file=wc" and "--block-depth=1.2". The# default block thickness (depth) is 0.5 angstrom. Again, file# "1ehz-wc.pml" combines the components to be ray-traced by PyMOL. pymol -qkc 1ehz-wc.pmlconvert -trim +repage -border 10 -bordercolor white 1ehz-wc-pymol.png 1ehz-wc.png # ------------------------------------------------------------------# 3. GUAA tetraloop mutant of sarcin/ricin domain from E. Coli 23S# rRNA -- 1msy, with minor groove in black and oriented in a bp# reference frame. x3dna-dssr -i=1msy.pdb --frame=A.2658+edge+wc -o=1msy-ok.pdb # set the viewx3dna-dssr -i=1msy-ok.pdb -o=tempx3dna-dssr -i=1msy-ok.pdb --block-file=minor+wc --block-depth=0.8 -o=1msy-ok-blocks.r3d # Note the options "--frame=A.2658+edge+wc" and# "--block-file=minor+wc".# The "1msy-ok.pml" file is for PyMOL rendering. pymol -qkc 1msy-ok.pmlconvert -trim +repage -border 10 -bordercolor white 1msy-ok-pymol.png 1msy-ok.png # ------------------------------------------------------------------# 4. 1msy, with blocks in outline mode. \cp 1msy-ok.pdb 1msy-edge.pdbx3dna-dssr -i=1msy-edge.pdb -o=tempx3dna-dssr -i=1msy-edge.pdb --block-file=edge -o=1msy-edge-blocks.r3d # Note the option "--block-file=edge", and file "1msy-edge.pml". pymol -qkc 1msy-edge.pmlconvert -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.
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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.
