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

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 modified coordinates as in the current state of the model:

commands (synonymous)	export the currently selected set of atoms, with modified 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 put in a variable data equivalent to what the write command would save to a file.

First parameter in the function is the format, second if needed is some qualifier, both matching what would be used in the command.

Examples:

a = write("xyz") #incorrect, not implemented, does not work
a = write("pdb") #incorrect, not implemented, does not work
a = write("mol") #exports to MOL v2000, original untransformed coordinates
a = write("v3000") #exports to MOL v3000, original untransformed coordinates
a = write("coord") #exports to XYZ, original untransformed coordinates
a = write("coord","mol") #exports to MOL v2000, transformed coordinates
a = write("coord","v3000") #exports to MOL v3000, transformed coordinates

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, in compressed form, 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.

Contributors

AngelHerraez