File formats/Export

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.

Pop-up menu

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.

Saving Jmol-specific files

Special image files PNGJ

Jmol can export to a PNG file that, in addition of a snapshot of the current molecular rendering, includes the state with all the information of rendering style (PNG) and, optionally, the data of the molecular model (PNGJ). These files appear as regular image files to any software but, when loaded back in Jmol (or drag-and-dropped) will reproduce the exact state of the 3D molecular model.

(The extra non-image information is included in a metadata area allowed by the png format)

Here are the basic commands; for additional options, see the documentation

commands
write image png "myFileName"	saves to disk a snapshot image of the current display, including also the state (notes 1, 2 and 3)
write "myFileName" as png	does the same as the above one
set imageState off; write image png "myFileName"	saves to disk a snapshot image of the current display, without the state (note 2)
write image pngj "myFileName"	saves to disk a snapshot image of the current display, including also the model, state and any files involved in the rendering (note 1)
write "myFileName" as pngj	does the same as the above one

(*) Note 1: if the specified file extension is not png, the file will still be a valid png image file, but it may or not be recognized by any software and may not be recognized by Jmol.

Note 2: by default, molecular state is included in the file, unless set imageState has been previously set to false or off.

Note 3: in the case of png files (not pngj), the molecular model file and any isosurface files involved must be in the same folder as the png file in order for the state to be interpreted.

New feature: Allows replacement of PNG data in PNGJ (available since version 14.31.34)

write "fileA.png" as pngj; saves a file containing both the image, the model data and the state

a = load("fileA.png",true); loads the file contents into a (binary) variable

b = load("fileB.png"); loads a regular image file into another (binary) variable

a._IMAGE_ = b._DATA_; puts the binary data making image "B" into the image section of data from file "A" (replacing the existing image data)

write var a "fileC.png"; saves the new combination stored in variable "a", i.e. molecular data from file "A" and image from file "B", into a new PNGJ file

Exporting for augmented reality software

Some users have produced models to be used in augmented reality (AR) software following one of these procedures using Blender:

• Open the model in Jmol, export as X3D,¹ import into Blender, retouch aspect, texture... and export to an FBX file. This latter format may be input into some AR software.

• Import directly a PDB file into Blender. Sometimes this results in a model with atoms but no bonds (since the PDB format does not necessarily include bond information). In this case, you may open the PDB file into Jmol and export as PDB,² then load this new file into Blender.

• For models available in other file formats like SDF, open them in Jmol and export as PDB,² then open in Blender.

Notes:

1. write ? as x3d

2. write ? as pdb

Contributors

AngelHerraez