Jmol Wiki - File formats/Coordinates

Jmol Wiki - File formats/Coordinates
File formats/Coordinates
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File Formats
General information
Coordinates
Chemical structure
Compressed
Converters
Images
Ray Tracing
Surfaces
3D Objects
Scripting
Exporting / saving files
Support for bond orders
Support for isotopes
Support for stereochemistry
File Formats for the Atomic Coordinates of the Molecule
These files are loaded into Jmol by either of the following methods:
using the application's topbar menu,
File > Open
will open a standard dialog for browsing local disk
File > Open URL
will ask for a location on the web
File > Get PDB
will ask for a 4-character PDB ID and retrieve the file from PDB at RCSB (see
Database Connection
File > Get MOL
will ask for some kind of supported chemical name or id and retrieve the file from Cactus Resolver at NCI (see
Database Connection
using the
load
command in the command line, in the Jmol scripting console, or in a script,
dragging and dropping the file onto the Jmol application window
Jmol will read any file and try to determine its format from its content. The file extension is not taken into account for identifying the format.
You can instruct Jmol as to which format to assume using this special command syntax:
load
fileFormat
::
fileName
where
fileName
includes the path, the file name itself and the file extension; paths may be absolute or relative; a full URL may also be used.
fileFormat
will be a keyword recognized by Jmol that designates that format. (Here is a
list of format values
Examples:
load mol::aspirin.txt
load pqr::1crn.pdb
load tinker::molecs/abc.txt
load molpro(xml)::ethanol.txt
What follows is a collection of specifications and comments on several formats, but is not a complete listing of all formats supported.
Feel free to add a subsection with a description of a format you know well.
Contents
File Formats for the Atomic Coordinates of the Molecule
1.1
MOL and SD
1.2
MOL2 (Sybyl, Tripos)
1.3
PDB
1.4
XYZ
1.5
CIF
1.6
mmCIF
1.7
Alchemy (Tripos)
1.8
GAMESS
1.9
Gaussian
1.10
Cube (Gaussian)
1.11
GROMACS
1.12
HIV / HIN (Hyperchem)
1.13
MOPAC
1.14
PQR
1.15
Amber
1.16
V3000 (Symyx MDL)
1.17
Q-Chem
1.18
JME
1.19
CASTEP
1.20
FHI-aims
1.21
DGRID
1.22
Z-matrix
1.23
KCF
1.24
SPARTAN, SMOL, SPARCHIVE
Exporting Coordinates
MOL and SD
MOL = MDL molfile = MOL v2000
SD = SDF = Structure Data Format
SD files share the MOL format but may contain several structures (separated by lines with $$$$), which will be read by Jmol as multiple models or frames.
MOLv3000 = extended molfile or extended connection table
This newer format applies to both MOL and SDF, hasn't got the 1000-atom limit and is also supported by Jmol.
Jmol reads MOL v2000 and v3000, and SD files (and can
write
them too).
Original from Molecular Design Limited, then Elsevier MDL, then Symyx Technologies, then BIOVIA Dassault Systèmes, widely adopted by many other programs.
Contains atom coordinates and bonds. V2000 (the most common) is limited to 1000 atoms.
These formats support formal charges and
isotopes
; both are read by Jmol. A variant used in PubChem adds partial charges using a custom field

, and this is also read by Jmol.
There are often MOL and SD files with two-dimensional data (i.e, all atoms have Z=0); Jmol will read them too, but the resulting flat model will not be realistic.
The defining tag (2D or 3D) must be located in line 2, columns 21-22, but is ignored by Jmol, which just uses the Z coordinates provided, be they zero or not.
Jmol has two ways to deal with such flat models:
you can run the
minimize
command
after loading; this will apply a simple UFF force field to reach a reasonable 3D structure;
or you can load the file using the
filter "2D"
switch
of the load command, in this way:
load myfile.mol filter "2D"
That will load the flat model and, before it is displayed, will add hydrogens if needed and then run a minimization; the result is a 3D model of the input 2D structure with a feasible conformation.
MOL header lines:
The first line is reserved for the molecule name and will be so used by Jmol in the popup menu.
The second line is in principle reserved for information on the originating program, date, user, etc. (Jmol will ignore this line).
The third line is for comments, and may contain an
inline script
starting with
jmolscript:
Official document (PDF):
2003 version
, copied
here
2015 version
(BIOVIA)
Some extra information on SD files at
US EPA DSSTox
Example files for MOL and SDF
v2000
and
v3000
MOL2 (Sybyl, Tripos)
Jmol reads MOL2 files.
Original from Tripos.
Contains atom coordinates, bonds, substructure information.
This format supports partial charges and
isotopes
, but only partial charges are currrently supported by Jmol.
A single MOL2 file may contain several structures, which will be read by Jmol as multiple models or frames.
Official document:
Example files
PDB
Jmol reads PDB files (and can write PDB files under some circumstances).
Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors. Can also contain temperature factor, formal charge, element symbol, alternate locations.
This format supports formal charges, and only hydrogen
isotopes
(as D and T); they are all read by Jmol.
If you need support for partial charges, see the similar
PQR format
below.
Files may contain an
inline script
starting with
REMARK jmolscript:
(Official Protein Data Bank document) Atomic Coordinate Entry Format.
Description:
Example files
Special use:
Jmol can get files directly from the Protein Data Bank website. See
Database_Connection
XYZ
Jmol reads XYZ files (and can write XYZ files under some circumstances). This format was originally from the XMol package, but has been widely adopted by many other programs. Contains only atom coordinates (no bonds) and, optionally, charges and vectors (e.g. for atom vibration). Supports multi-model data (multi-frame, animations).
An extension of this format supports
isotopes
, and they are read by Jmol.
XYZ header lines:
The first line is reserved for the number of atoms.
The second line is for comments, and may contain an
inline script
starting with
jmolscript:
Example
by Paul Bourke.
Example files
Details about the XYZ format
CIF
Jmol reads CIF files.
Crystallographic Information File, the official format from the International Union of Crystallography:
v. 1.0
Original documentation
Acta Crystallographica
47
: 655-685 (1991)
doi:10.1107/S010876739101067X
v. 1.1 the
2003 update
CIF files may contain an
inline script
starting with
#jmolscript:
Example files
Special use:
Jmol can get files directly from the ligand collection at the Protein Data Bank website. See
Database_Connection#PDB
mmCIF
Jmol reads mmCIF files.
Macromolecular Crystallographic Information File, an expanded format to cope with macromolecules.
Official documentation
Example files
Alchemy (Tripos)
Jmol does not fully support reading of Alchemy and Alchemy2000 files. A simple Alchemy reader is implemented starting Jmol 11.7.18.
Alchemy example
and
Alchemy2000 description
by Paul Bourke.
A complete specification of these formats would be needed to fully implement the reader. If you have those details, please contact the developers team.
Example files
supported by Jmol.
GAMESS
Jmol reads GAMESS files (General Atomic and Molecular Electronic Structure System, by Gordon research group at Iowa State University).
Official documentation
Example files
Gaussian
Jmol reads only the output format.
Recent versions of Jmol application can also export to files in Gaussian input format.
There are
example files
of Gaussian input, output and log.
Cube (Gaussian)
Jmol reads Cube files, original from Gaussian software (
Gaussian website
).
Description of Cube Input and Cube Output formats:
Description
by Paul Bourke.
Example files
GROMACS
Jmol (11.7.47 or later) reads GRO files; coordinates are assumed to be in nanometers; data are read as if a PDB file, with secondary structure assigned automatically and elements inferred from atom names. UREA and SOL are included in the
solvent
set.
Also, force vectors are read and included as vibrations (activated by default on file load).
File format is called
gro
or
Gromos87
. Usual extension is
.gro
Description
of the format.
Example files
Utilities:
You can convert from
gro
to
pdb
using the
editconf
program, which is a part of the GROMACS package that can be run from the command line:
editconf -f whatever.gro -o whatever.pdb
You can also use the
trjconv
utility, included in the GROMACS installation. It will read a GROMACS trajectory file (.xtc or .trr) and output a .pdb file. So:
Use trjconv to generate a .pdb file.
Load the .pdb file into Jmol (using the
trajectory
option) and animate.
HIV / HIN (Hyperchem)
Jmol reads HIV (or HIN) files, the native format of Hyperchem, a software sold by
Hypercube Inc.
Example
by Paul Bourke, and other
example files
Details of HIN format
MOPAC
Jmol reads
mopout
output files from
MOPAC
and the new
graphf
output from MOPAC2007 (
.mgf
files), which
contains coordinates, charges, and molecular orbitals.
openMOPAC, Molecular Orbital PACkage, public domain.
Example files
PQR
Jmol reads and writes PQR files. However, since they are very similar to
pdb
files, they may be misread.
Version support
: reading
pqr
started at Jmol v. 11.1.30; writing
pqr
files started at v. 12.3.2
If the file contains a line that starts with "REMARK 1 PQR" (3 spaces before the '1', one after it), it will be interpreted as
pqr
format. Otherwise, Jmol will interpret it as a
pdb
file (and so will not get the charge and radii correct). To force the file be read as
pqr
, add
pqr::
just before the filepath in the
load
command, like this:
load pqr::somePath/someFileName.pqr
pqr
is a format based on
pdb
, where the
occupancy
is replaced with the atomic charge and the
temperature
(or
B factor
) is replaced with atomic radius (however, the column positions in many pqr files do not match those of pdb files). This gives the acronym:
for pdb,
for charge,
for radius. Jmol interprets the charge values (property
partialcharge
) and the radii (property
vanderwaals
), and can hence use them e.g. in
color atoms partialCharge
and
spacefill
The
pqr
format has somewhat uncertain origins, but is used by several computational biology packages, including MEAD, AutoDock and
APBS
, for which it is the primary input format.
PQR format description
Note that APBS reads PQR loosely, based only on white space delimiters, but Jmol may be more strict about column positions.
Ideally, one should follow the PDB specifications, which are:
pdb
occupancy
/ pqr
charge
: columns 55 to 60, decimal point at 58.
pdb
B-factor
/ pqr
radius
: columns 61 to 66, decimal point at 64.
pdb
files can be converted to
pqr
by the
PDB2PQR
software, which adds missing hydrogen atoms and calculates the charge and radius parameters from a variety of force fields.
Example files
Amber
Jmol (11.7 or later) reads molecular dynamics output files from
Amber
. The fileset must have a structure like:
1 (topology file) + n (coordinate files)
The
filter
option of the
load
command can be used, as well as a new option to allow selective "first,last,step" loading of coordinate trajectories.
(This is preliminary and needs testing)
You can see an
example
Example files
V3000 (Symyx MDL)
See
MOL
Q-Chem
Jmol reads files output from the computational chemistry package Q-Chem. See the
Q-Chem specific section
Example files
JME
This is the native format from
JME Molecular Editor
(by Peter Ertl).
See
File_formats/Chemical_Structure#JME
CASTEP
Jmol (11.8) can read
.cell
files in the
CASTEP
format (only periodic boundary conditions).
CASTEP is a software package which uses density functional theory to provide a good atomic-level description of all manner of materials and molecules.
FHI-aims
Jmol (11.8) can read
geometry.in
files in the
FHI-aims
format (both cluster models and periodic boundary conditions).
FHI-aims (from Fritz-Haber-Institut der Max-Planck-Gesellschaft) is an all-electron electronic structure code based on numeric atom-centered orbitals.
DGRID
Jmol (11.9.14) can read DGRID files; this format is a generalized representations of output from a variety of quantum mechanical calculation packages, including especially ADF (Amsterdam Density Functional).
Z-matrix
Jmol (12.3.7) can open files with
Z-matrix data
, an
internal coordinate representation, that provides for each atom its element symbol, bond lengths, bond angles and dihedral angles.
This format is used e.g. by the MOPAC (
Molecular Orbital PACkage
) programs.
This format will be assumed when reading a file whose content starts with
#ZMATRIX
or by using
load zmatrix::myFileName
Any line that starts with # will be taken as a comment (and it can contain an
inline script
). Blank lines are ignored.
Any position number may be replaced by a unique atom name+number (as in example number 3 below).
Dummy atoms are allowed, using X or Xn.
Bond order may be specified as an additional integer on the line.
Examples:
#ZMATRIX
# methane
H  1 1.089000
H  1 1.089000  2  109.4710
H  1 1.089000  2  109.4710  3  120.0000
H  1 1.089000  2  109.4710  3 -120.0000
#ZMATRIX
# carbon dioxide
O  1 1.3000               2Â
O  1 1.3000    2  180     2
#ZMATRIX
# carbon dioxide
C1
O1 C1 1.3000             2
O2 C1 1.3000  O1  180    2
#ZMATRIX
# ammonia (using simple angles only)
# Negative distance indicates that the second angle is a normal angle, not a dihedral:
N1
H1 N1 1.0
H2 N1 1.0 H1 107Â
H3 N1 -1.0 H1 107 H2 107
#ZMATRIX
# ammonia (using simple angles only)
# Negative distance and one negative angle reverses the chirality:
N1
H1 N1 1.0
H2 N1 1.0 H1 107
H3 N1 -1.0 H1 -107 H2 107
KCF
This format is not supported by Jmol
These notes are here for future reference.
KCF (KEGG Chemical Function) format is the standard used by the
Kyoto Encyclopedia of Genes and Genomes (
KEGG
) and the Resource for Informatics of Glycomes at Soka (
RINGS
). It is somewhat similar to the
mol
format.
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. M. Hattori, Y. Okuno, S. Goto, M. Kanehisa (2003)
Journal of the American Chemical Society
125
:11853-11865 PMID:14505407 doi:10.1021/ja036030u
SPARTAN, SMOL, SPARCHIVE
Jmol can read these, which are proprietary formats of the Spartan software by
WaveFunction
See
some examples
of these files.
Exporting Coordinates
Jmol has a limited capability for writing molecular coordinates, including only the currently selected set of atoms. (This allows to save the whole model, maybe in a format different from the original one, or to extract a subset of the atoms in the original model).
Due to Java security restraints, only the
application
and the
signed applet
can write to files on disk.
The unsigned applet can however display the exported data in the console window, from where you can copy it, paste into a text editor and save it to file.
Only
MOL, XYZ and PDB
formats are supported for export. The method is to use the
write
command
(from script or from the console).
The
application
and the
signed applet
also allow to save a
copy
of the loaded file (any format) via the pop-up menu >
File
The application can also export to
Gaussian input
format using the top menu and a dialog.
Contributors
AngelHerraez
Pbourke
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This page was last edited on 17 February 2023, at 16:52.
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