DSSR-enabled cartoon-block schematics with PyMOL

A tutorial page [Home]

Introduction

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.

Input a PDB id

Pre-calculated cartoon-block images together with summary information and DSSR-derived structural features in human-readable text and machine-friendly JSON formats are available for all nucleic-acid-containing structures in the PDB. Note that for gigantic structures like ribosomes that are only represented in mmCIF format, no schematics are included in this resource. The base block images are most effective for small to medium-sized structures.

Here are a few examples.

1ehz, the crystal structure of yeast phenylalanine tRNA at 1.93-Å resolution
2lx1, the major conformation of the internal loop 5'GAGU/3'UGAG
2grb, the crystal structure of an RNA quadruplex containing inosine tetrads
4da3, the crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41
1oct, the crystal structure of the Oct-1 POU domain bound to an octamer site
2hoj, the crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions

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 --blocview option. The corresponding PyMOL session file and PDB coordinate file are available for download. One can also visualize the structure interactively via 3Dmol.js.

Sample PDB entries

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.

Specify a coordinate file

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.

Web API help message

  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]
    raw_xyz=true-or-FALSE(default)        [e.g., raw_xyz=true]
    type=output-in-json-or-text           [e.g., type=json]
Required parameter
    url=URL-to-coordinate-file [e.g., url=https://files.rcsb.org/download/1ehz.pdb.gz]
    model=@coordinate-file     [e.g., model=@1ehz.pdb]
    # 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
    curl http://skmatic.x3dna.org/api -F 'model=@1ehz.pdb' -F 'block_file=wc-minor'
    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 -F 'url=https://files.rcsb.org/download/1ehz.pdb.gz' -F 'type=json'
    curl http://skmatic.x3dna.org/api/pdb/1ehz -o 1ehz.png
    curl http://skmatic.x3dna.org/api/pdb/1ehz/json