File formats/Export

From Jmol
Jump to navigation Jump to search

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 xyz myFile.myExt
write myFile.myExt as xyz
File icon.gifxyz format
write myFile.pdb
write pdb myFile.myExt
write myFile.myExt as pdb
File icon.gifpdb format
write myFile.mol
write mol myFile.myExt
write v2000 myFile.myExt
write myFile.myExt as mol
write myFile.myExt as v2000
File icon.gifmol-v2000 format
write v3000 myFile.myExt
write myFile.myExt as v3000
File icon.gifmol-v3000 format
write myFile.sdf
write sdf myFile.myExt
write myFile.myExt as sdf
File icon.gifsdf-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 (File icon.gifpng 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 File icon.gifpng 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
File icon.gifmol-v2000 format
write coord v3000 myFile.myExt
File icon.gifmol-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:

a = write("xyz")
exports to File icon.gifxyz format
a = write("pdb")
exports to File icon.gifpdb 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 File icon.gifmol-v2000 or File icon.gifmol-v3000 format, respectively
a = write("coord")
exports to File icon.gifxyz format, original untransformed coordinates
a = write("coord","mol")
exports transformed coordinates to File icon.gifmol-v2000 or File icon.gifmol-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")


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

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