NGL@1.0.0-beta.7 Home Manual Reference Source Gallery

File Formats

The following file formats are supported. Files can be compressed with gzip. Format detection is based on the file extension.

Structures

Structure data is saved into Structure instances.

Loading flags (in the GUI available from the File menu):

Atom data added to all structures:

mmCIF

Extension: .mmcif, .cif, .mcif

Specification: http://mmcif.wwpdb.org/

Supported features:

PDB/PQR

Extension: .pdb, .ent, .pqr

Specification: http://www.wwpdb.org/documentation/file-format.php

Supported features:

GRO

Extension: .gro

Specification: http://manual.gromacs.org/current/online/gro.html

Supported features:

TODO:

SDF

Extension: .sdf, .sd

Specification: http://download.accelrys.com/freeware/ctfile-formats/

Supported features:

MOL2

Extension: .mol2

Specification: http://www.tripos.com/data/support/mol2.pdf

Supported features:

MMTF

Extension: .mmtf

Specification: https://github.com/rcsb/mmtf

Supported features:

Topologies

Topology are different from structure files as they not contain coordinate data.

PRMTOP

Topology format used by Amber.

Extensions: .prmtop, .parm7

PSF

Topology format used by Charmm.

Extension: .psf

TOP

Topology format used by Gromacs.

Extension: .top

Trajectories

Structure files in mmCIF, PDB, GRO, SDF, MOL2 or MMTF format can also be loaded as trajectories by setting the asTrajectory flag. Trajectory files in DCD, NCTRAJ, TRR or XTC format are added to a Structure.

DCD

Uncompressed, binary trajectory format used by Charmm.

Extension: .dcd

TRR

Uncompressed, binary trajectory format used by Gromacs.

Extension: .trr

NCTRAJ

Uncompressed, binary trajectory format used by Amber.

Extensions: .nctraj, .ncdf, .nc

XTC

Compressed, binary trajectory format used by Gromacs.

Extension: .xtc

Densities

Density data is saved into Volume instances.

MRC/MAP/CCP4

Extensions: .mrc, .map, .ccp4

Specification: http://www.ccp4.ac.uk/html/maplib.html, http://ami.scripps.edu/software/mrctools/mrc_specification.php

Supported features:

CUBE

Extensions: .cube, .cub

Specification: http://paulbourke.net/dataformats/cube/

Supported features:

TODO:

DSN6/BRIX

Extensions: .dsn6, .brix

Supported features:

DX/DXBIN

Extensions: .dx, .dxbin

Specification: http://www.poissonboltzmann.org/docs/file-format-info/

Supported features:

XPLOR/CNS

Extensions: .xplor, .cns

Supported features:

Surfaces

The surface geometry is saved into Surface instances.

OBJ

Extension: .obj

The PyMOL molecular visualization system can export surfaces in the OBJ format.

PLY

Extension: .ply

The EDTsurf program outputs surfaces in the PLY format.

Annotation

wwPDB Validation Report

Extension: .xml

Load PDB entry 3PQR and its validation report. Add the validation object to the structure object. Then show clashes and color by geometry quality using the ValidationRepresentation to show the clash data. There are two validation dta-based colorschemes available: densityfit and geoquality.

Promise.all( [
    stage.loadFile( "rcsb://3PQR" ),
    NGL.autoLoad( "http://ftp.wwpdb.org/pub/pdb/validation_reports/pq/3pqr/3pqr_validation.xml.gz", { ext: "validation" } )
] ).then( function( ol ){
    ol[ 0 ].structure.validation = ol[ 1 ];
    ol[ 0 ].addRepresentation( "cartoon", { color: "geoquality" } );
    ol[ 0 ].addRepresentation( "validation" );
    ol[ 0 ].addRepresentation( "ball+stick", {
        sele: ol[ 1 ].clashSele,
        color: "geoquality"
    } );
    ol[ 0 ].addRepresentation( "licorice", {
        sele: "hetero",
        color: "geoquality"
    } );
    stage.autoView();
} );

General

JSON

Extension: .json

CSV

Extension: .csv

MSGPACK

Extension: .msgpack

NETCDF

Extension: .netcdf

TXT

Extensions: .txt, .text

XML

Extension: .xml