ribbon's Introduction

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

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ribbon's Issues

PDB/PDBx parser

I don't actively maintain this code any more, but there are working PDB and PDBx (using the underlying CIF format) parsers here if you're interested: https://github.com/TuftsBCB/io

I'm not necessarily suggesting you use them directly, but they may be helpful in other ways!

Api-gateway

Personally, I like your work but used your code as API-gateway (direct access to the functions). Please change access from private to public. It's my humble request Thankyou

HI, I've built this on a low memory embedded system and it runs out of memory when rendering. I noticed in your example code that it renders a 1920x1080 image, is this default? How can I specify image size or optimise for low memory system?

Thanks.

Missing residues

Some residues at the beginning and at the end of the chains are missing in the mesh.

If you compare a cartoon mesh from pymol/VMD/avogadro... and the mesh created by ribbon.go, you can see that some parts are missing.

For example :

Beginning of the chain:

End of the chain

Recommend Projects

fogleman / ribbon Goto Github PK