Eugene

Dear Angel, I'm deeply sorry for inconvinience because my first message was not correct, and I didn't found the way how to edit original message, hence I've report about my mistake in first answer to the original message (see above). In fact the problem are not in the zip, rather than how CUBE format opens in Jmol. Let me explain (in short) about the CUBE format. There are two sections in the file, first one related to atomic positions and the second section is isosurface related. When I open CUBE...

Finally the best way to convert CUBE to JVXL format and save to zip is to use jmolscript by invoking Jmol.jar. The final version of convers could be downloaded here (for cube to zip, bash script): https://github.com/ladyteam/LADYtools/blob/master/cube2jvxl.sh and here (XSF format to CUBE, python3 code): https://github.com/ladyteam/LADYtools/blob/master/xsf2cube.py Hope some one find these converters useful. I'm really appreciated for your helpful advices, thank you so much! p.s. Tested with Jmol...

Oh, after writing zip with JMOL console write ZIP "filename.zip" command I gues I've found, that additional JmolManifest.txt file is need with script filename inside. At least it working. Thank you Bob!

But for some reason zip can't be loaded correctly, first I zip all three files: zip file.zip file.spt file.xyz file.jvxl The content of file.spt is: load "file.xyz" isosurface "file.jvxl" then I run in Jmol console load "file.zip" and finally I have error message: Unrecognized file format for file.zip|file.spt load "file.xyz" isosurface "file.jvxl" Maybe I have to put some other command in JMOL console to load script in side zip?

Dear Bob, Thank you for the very helpfull answer. Indeed it is possible to extract both atomic position data (into XYZ format) and convert isosurface data into JVXL format, and then write a jmol script file to sequentially load of atomic positions and isosurface data. It seems to work nicely. But one have to always keep in mind, converting into JVXL will lead to lost volumetric CUTOFF parameter, so this parameter should be set up properly before converting to JVXL. Finally it's a little bit complicated...

Dear Angel, I'm deeply sorry for inconvinience because my first message was not correct, and I didn't found the way how to edit original message, hence I've report about my mistake in first answer to the original message (see above). In fact the problem are not in the zip, rather than how CUBE format opens in Jmol. Let me explain (in short) about the CUBE format. There are two sections in the file, first one related to atomic positions and the second section is isosurface related. When I open CUBE...

Oops, I'm sorry. Jmolscript is OK. There is the other problem. When I open the CUBE file in Jmol (using open in menu file) only surface is plotted but no atoms, and the surface do not react on offset option, i.e. if I put the command: isosurface cutoff 0.1; isosurface cutoff 0.2; nothing happens. Everything good if I put these commands in console: $ load "w90_00001.cube" $ isosurface s1 sign cyan yellow cutoff 0.5 "w90_00001.cube" color translucent 0.45 It would be nice these commands run automaticaly...

jmolscript with zipped data (and xsf file format)