File formats/Export
Contents
Exporting or saving molecular model files from Jmol
Although Jmol was designed as a viewer, it has now capabilities to save files for the displayed molecular model (or a subset of it).
write command
Jmol can export the currently selected set of atoms to a file in
- XYZ format
- PDB format
- MOL v2000 format (single model)
- MOL v3000 format (single model)
- SDF v2000 format (single or multiple models)
The last 3 are according to the official format specification from MDL-Accelrys-Symyx.
The syntax (see reference documentation) is like this:
| commands (synonymous) | export the currently selected set of atoms,
with original coordinates, using this format: |
|---|---|
write myFile.xyz write xyz myFile.myExt write myFile.myExt as xyz |
 xyz format
|
write myFile.pdb write pdb myFile.myExt write myFile.myExt as pdb |
pdb format
|
write myFile.mol write mol myFile.myExt write v2000 myFile.myExt write myFile.myExt as mol write myFile.myExt as v2000 |
mol-v2000 format
|
write v3000 myFile.myExt write myFile.myExt as v3000 |
mol-v3000 format
|
write myFile.sdf write sdf myFile.myExt write myFile.myExt as sdf |
sdf-v2000 format
|
write myFile.jmol write jmol myFile.myExt write myFile.myExt as jmol |
writes a single file that packs the original model file, the state as a Jmol script, and a snapshot (png image) of the current display; this file may be loaded back into Jmol and will reproduce the state
|
write image pngj myFile.png write myFile.png as pngj |
functionally equivalent to the previous one, but produces a png file that is displayed as a regular image in any software; when loaded into Jmol it will read the model and its state
|
All of the above commands will save the original cooordinates of each atom as they were in the input file.
There is also the choice (only in MOL format) of saving the transformed coordinates as they are in the current state of the model:
| commands (synonymous) | export the currently selected set of atoms,
with transformed coordinates, using this format: |
|---|---|
write coord myFile.mol write coord mol myFile.myExt |
mol-v2000 format
|
write coord v3000 myFile.myExt |
mol-v3000 format
|
write() function
This function in the Jmol Scripting Language allows to place the output of the write command into a variable, rather than saving to a file. The data can later be loaded using load var a.
See also show() below, as an alternative.
First parameter in the function is the format, second if needed is some qualifier, both matching what would be used in the command.
Common examples:
| commands | |
|---|---|
a = write("xyz")
|
exports to xyz format
|
a = write("pdb")
|
exports to pdb format; note that Jmol will read back this format, but it is not compliant with the official PDB standard
|
a = write("mol")
a = write("v3000")
|
exports to mol-v2000 or mol-v3000 format, respectively
|
a = write("coord")
|
exports to xyz format, original untransformed coordinates
|
a = write("coord","mol")
|
exports transformed coordinates to mol-v2000 or mol-v3000 format, respectively
|
a = write("jmol")
|
exports a packed file that contains the model and the state (but not the snapshot)
(only available since Jmol 14.27) |
show() chemical function
The same information that would be exported to a file may be put into a variable using this function. It uses the NCI CACTVS Resolver web service for format conversion, and hence it needs a live internet connection to work.
- Available since Jmol version 14.6.0
- Note: If only a subset of the full model has been selected, only that subset will be included in the exported model. Since the procedure involves a query to the Resolver, and their server tries to interpret it as a full molecule, the result may then not be what you expect. Example:
select _N; show("chemical mol")returns mol-formatted data for ammonia, no matter which was the original molecule containing several N atoms.
Formats available are:
alc
|
Alchemy (Tripos) | cdxml
|
XML-compliant version of ChemDraw's native file format | cerius
|
Cerius II from Accelrys/MSI |
|---|---|---|---|---|---|
charmm
|
CHARMM (Chemistry at HARvard Macromolecular Mechanics) | cif
|
Crystallographic Information File | cml
|
Chemical Markup Language |
ctx
|
Gasteiger group | gjf
|
Gaussian input | gromacs
|
GROMACS |
hyperchem
|
HIV / HIN format from Hyperchem | jme
|
from the JME/JSME Molecular Editor | maestro
|
from Schrödinger |
mol
|
Symyx MDL | mol2
|
Sybyl, Tripos | sybyl2
|
Sybyl, Tripos |
mrv
|
Marvin format, from ChemAxon | pdb
|
from Protein DataBank, but nonstandard | sdf
|
Symyx MDL |
sdf3000
|
Symyx MDL, V3000 | sln
|
SYBYL Line Notation | smiles
|
SMILES string |
xyz
|
the traditional XYZ format |
The syntax is like this:
d = show("chemical xyz")
d = show("chemical mol")
d = show("chemical hyperchem")
etc.
The result (text string as the value of the variable) may then be displayed, processed, or even may be written to a file using
write var d myFile.hin. In this way, Jmol is in fact exporting file formats that it cannot export natively, by using the format conversion server at NCI.
These are available:
File > Save > Save a copy of file
File > Save > Save as PNG/JMOL (image+zip)
File > Save > Save JVXL isosurface
File > Export > Export PNG+JMOL image
The 2nd and 4th are equivalent and contain, packed in a single file, a snapshot PNG image, the coordinates file and the state script file.
Save isosurface
The pop-up menu entry will svae the last isosurface selected or generated. More flexibility is allowed by using the write isosurface command.
