File formats/Export

From Jmol

Jump to: navigation, 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

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")
a = write("pdb")
incorrect, not implemented, do not work
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)

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.

Personal tools