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).
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:
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
write coord v3000 myFile.myExt
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.
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.
The pop-up menu entry will svae the last isosurface selected or generated. More flexibility is allowed by using the
write isosurface command.