Protein Ribbon Diagrams

Parse PDB files and render ribbon diagrams of proteins in pure Go.

Installation

Go should be installed and your GOPATH should be set (defaults to $HOME/go in Go 1.8+). $GOPATH/bin should be on your $PATH if you want to run the binaries easily.

$ go get -u github.com/fogleman/ribbon/cmd/rcsb

Example Usage

Provide a 4-digit RCSB Structure ID. The PDB file will automatically be downloaded and an image will be rendered. The triangle mesh will also be saved.

$ rcsb 4hhb  # generates 4hhb.png and 4hhb.stl

Resources

RCSB Protein Data Bank - Find PDB files of proteins here. Over 100,000 in the database.

PDB File Format - Details on the PDB file format.

Package pdb

Documentation

The pdb package parses PDB files. The following entities are currently parsed:

ATOM   => *pdb.Atom
HETATM => *pdb.Atom
CONECT => *pdb.Connection
HELIX  => *pdb.Helix
SHEET  => *pdb.Strand
BIOMT  => pdb.Matrix
SMTRY  => pdb.Matrix

Additionally, some higher-level constructs are produced:

*pdb.Residue
*pdb.Chain

Package ribbon

Documentation

The ribbon package generates 3D meshes given a pdb.Model. It can produce the following types of meshes:

• Ribbon
• Ball & stick (for ligands)
• Space filling
• Backbone

Package fauxgl

The fauxgl library is used for rendering the 3D meshes in pure Go.

Samples