A tutorial page created by Dr. Xiang-Jun Lu <firstname.lastname@example.org>
This website (see screenshot below) aims to showcase DSSR-enabled cartoon-block schematics of nucleic acid structures using PyMOL. It presents a simple interface to browse pre-calculated PDB entries with a set of default settings: long rectangular blocks for Watson-Crick base-pairs, square blocks for G-tetrads in G-quadruplexes, with minor-groove edges in black. Users can also specify a URL to a PDB- or mmCIF-formatted file or upload such an atomic coordinates file directly, and set several common options to customerize the rendered image.
Moreover, a web API to DSSR-PyMOL schematics is available to allow for its easy integration into third-party tools.
Pre-calculated cartoon-block images together with summary information are available for PDB entries of nucleic-acid-containing structures. Note that gigantic structures like ribosomes that are only represented in mmCIF format are excluded from this resource. The base block images are most effective for small to medium-sized structures.
Here are a few examples.
Each entry is shown with images in six orthogonal
perspectives (front, back, right, left, top, and bottom)
which can be downloaded as a tarball. The 'front' image
(upper-left in the panel) is oriented into the
most-extended view with the DSSR
The corresponding PyMOL session file and PDB coordinate
file are available for download. One can also visualize
the structure interactively via
Users can browse random samples of pre-calculated PDB entries. The number should be between 3 and 99, with a default of 12 entries (see below for an example). Simply click the 'Submit' button or an example link to see sample results.
The atomic coordinate file must be in PDB or mmCIF format,
and can be optionally gzipped (
.gz). One can
either specify a URL to a coordinate file or select a
local one to upload. Several common options are available
for user customizations.
Usage http://skmatic.x3dna.org/api [options] url=|model@ http://skmatic.x3dna.org/api/pdb/pdb_id -- for a pre-calculated PDB entry http://skmatic.x3dna.org/api/help -- display this help message Options block_file=styles-in-free-text-format [e.g., block_file=wc-minor] block_color=nt-selection-and-color [e.g., block_color='A:pink'] block_depth=thickness-of-base-block [e.g., block_depth=1.2] r3d_file=true-or-FALSE(default) [e.g., r3d_file=true] raw_xyz=true-or-FALSE(default) [e.g., raw_xyz=true] Required parameter url=URL-to-coordinate-file [e.g., url=https://files.rcsb.org/download/1ehz.pdb.gz] model@coordinate-file [e.g., email@example.com] # Only one must be specified. 'url' precedes 'model' when both are specified. # The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped. Examples http -f http://skmatic.x3dna.org/api block_file='wc-minor' firstname.lastname@example.org r3d_file=t http -f http://skmatic.x3dna.org/api url=https://files.rcsb.org/download/1ehz.pdb.gz -d -o 1ehz.png http http://skmatic.x3dna.org/api/pdb/1ehz -d -o 1ehz.png # with 'curl' curl http://skmatic.x3dna.org/api -F 'email@example.com' -F 'block_file=wc-minor' -F 'r3d_file=1' curl http://skmatic.x3dna.org/api -F 'url=https://files.rcsb.org/download/1ehz.pdb.gz' -o 1ehz.png curl http://skmatic.x3dna.org/api/pdb/1ehz -o 1ehz.png