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):

• asTrajectory: load the topology from first model and add the coordinates from it and the remaining models as trajectory frames. Note that this assumes that all models share the same topology.
• firstModelOnly: load only the first model.
• cAlphaOnly: load only C-alpha atoms.

Atom data added to all structures:

• index: running atom index that is unique within the structure
• modelindex: running model index that is unique within the structure
• globalindex: globally unique running atom index

mmCIF

Extension: .mmcif, .cif, .mcif

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

Supported features:

• Title: read from "_struct.title" item
• Box coordinates: read from "_cell" item
• Space group: read from "_symmetry.space_group_name_H-M" item
• Secondary structure: read from "_struct_conf" and "_struct_sheet_range" items
• Assemblies
  • Biological assemblies: read from "_pdbx_struct_oper_list" and "_pdbx_struct_assembly_gen" items
  • Non-crystallographic symmetry: read from "_struct_ncs_oper" item
  • Crystallographic symmetry: determined from space group
• Atom data: read from the "_atom_site" items
  • resname: read from "label_comp_id" field
  • x, y, z: read from "Cartn_x", "Cartn_y", "Cartn_z" fields
  • resno: read from "auth_seq_id" field
  • serial: read from "id" field
  • atomname: read from "label_atom_id" field
  • chainname: read from "auth_asym_id" field
  • element: read from "type_symbol" field or deduced from atomname if not available
  • vdw: deduced from element
  • covalent: deduced from element
  • bfactor: read from "B_iso_or_equiv" field
  • altloc: read from "label_alt_id" field
  • inscode: read from "pdbx_PDB_ins_code" field
  • hetero: determined from "group_PDB" field, which is "ATOM" or "HETATM"
  • occupancy: read from "occupancy" field
• Connectivity: read from the "_struct_conn" item, which generally contains data on hetero atom connectivity. Entries with "_conn_type_id" equal to "hydrog" are currently ignored. Connectivity for non-hetero atoms is calculated during post-processing.
• The cif dictionary is added to the structure.extraData property, with key cif, excluding "_atom_site" items

PDB/PQR

Extension: .pdb, .ent, .pqr

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

Supported features:

• Title: read from "TITLE" record
• Box coordinates: read from "CRYST1" record
• Space group: read from "CRYST1" record
• Secondary structure: read from "HELIX" and "SHEET" records
• Assemblies
  • Biological assemblies: read from "REMARK 350" record
  • Non-crystallographic symmetry: read from "MTRIX" record
  • Crystallographic symmetry: determined from space group
• Atom data: read from the "ATOM" and "HETATM" records
  • resname: read from "resName" field
  • x, y, z: read from "x", "y", "z" fields
  • resno: read from "resSeq" field
  • serial: read from "serial" field
  • atomname: read from "name" field
  • chainname: read from "chainID" field
  • element: read from "element" field or deduced from atomname if not available
  • vdw: deduced from element
  • covalent: deduced from element
  • bfactor: read from "tempFactor" field
  • altloc: read from "altLoc" field
  • inscode: read from "insCode" field
  • hetero: determined from record type, which is "ATOM" or "HETATM"
  • occupancy: read from "occupancy" field
• Connectivity: read from the "CONNECT" record, which generally contains data on hetero atom connectivity. Connectivity for non-hetero atoms is calculated during post-processing.

GRO

Extension: .gro

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

Supported features:

• Title: read from "title string" field
• Box coordinates: read from "box vectors" field
• Secondary structure: not available in the format, automatically calculated during post-processing
• Atom data:
  • resname: read from "residue name" field
  • x, y, z: read from "position" fields
  • resno: read from "residue number" field
  • serial: read from "atom number" field
  • atomname: read from "atom name" field
  • chainname: not available, automatically assigned during post-processing
  • element: deduced from atomname
  • vdw: deduced from element
  • covalent: deduced from element
  • altloc: not available, left empty
  • inscode: not available, left empty
• Connectivity: not available in the format, automatically calculated during post-processing

TODO:

• Read velocity data from GRO files that includes it (and create a new Representation to display it).

SDF

Extension: .sdf, .sd

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

Supported features:

• Title: read from the second line of the header block
• Box coordinates: not available in the format
• Secondary structure: not available in the format, automatically calculated during post-processing
• Atom data:
  • resname: not available, set as "HET"
  • x, y, z: read from "position" fields
  • resno: read from "residue number" field
  • serial: not available, set from running index
  • atomname: not available set as "element + index"
  • chainname: not available, automatically assigned during post-processing
  • element: read from "element" field
  • vdw: deduced from element
  • covalent: deduced from element
  • altloc: not available, left empty
  • inscode: not available, left empty
• Connectivity: read from bond block, includes bond order
• Associated data items are added to the structure.extraData property with key sdf

MOL2

Extension: .mol2

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

Supported features:

• Title: read from the first line of the molecule record
• Box coordinates: not available in the format
• Secondary structure: not available in the format, automatically calculated during post-processing
• Atom data:
  • resname: read from "residue name" field
  • x, y, z: read from "coordinate" fields
  • resno: read from "residue number" field
  • serial: read from "atom number" field
  • atomname: read from "atom name" field
  • chainname: not available, automatically assigned during post-processing
  • element: read from "atom type" field
  • vdw: deduced from element
  • covalent: deduced from element
  • altloc: not available, left empty
  • inscode: not available, left empty
  • bfactor: read from the "partial charge" field (i.e. not a bfactor)
• Connectivity: read from bond record, includes bond order

MMTF

Extension: .mmtf

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

Supported features:

• Title: read from "title"
• Box coordinates: read from "unitCell" field
• Secondary structure: read from "secStructList" field
• Atom data:
  • resname: read from "groupTypeList[].groupName" field
  • x, y, z: read from "x/y/zCoordList" fields
  • resno: read from "groupIdList" field
  • serial: read from "atomIdList" field
  • atomname: read from "groupTypeList[].atomNameList" field
  • chainname: read from "chainNameList" field
  • element: read from "groupTypeList[].elementList" field
  • vdw: deduced from element
  • covalent: deduced from element
  • altloc: read from "altLocList" field
  • inscode: read from "insCodeList" field
  • bfactor: read from "bFactorList" field
  • occupancy: read from "occupancyList" field
• Connectivity: read from "bondAtomList", "bondOrderList" fields and their "groupTypeList[]" counterparts

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:

• Header data
• Density data

CUBE

Extensions: .cube, .cub

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

Supported features:

• Header data
• Density data

TODO:

• Read structure embedded in the header.

DSN6/BRIX

Extensions: .dsn6, .brix

Supported features:

• Header data
• Density data

DX/DXBIN

Extensions: .dx, .dxbin

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

Supported features:

• Header data
• Density data

XPLOR/CNS

Extensions: .xplor, .cns

Supported features:

• Header data
• Density data

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