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#52 (.jmol?) problems going from v5 -> v6, v7

Dietrich Bartel

In version 5 Atom properties could be edited/changed. This is not possible with v6 and v7. In v5
atom properties were found in .jmol/properties. The property table is saved in v6 and v7 under
.jmol/jmol_atomtypes.txt. When starting jmol without having .jmol/jmol_atomtypes.txt v7 complains
about it with "readAtomTypes getResourceAsStream: jmol_atomtypes.txt" wheras v6 doesn't
complain. v6 and v7 do read the history file (recent files, POVRAY path ...) but they don't update
the recent files (povray path is updated!)


  • Logged In: YES

    Thanx for reporting this. I will look into this problem.

    • assigned_to: nobody --> egonw
    • summary: (.jmol?) problems going from v5 -> v6, v7 --> (.jmol?) problems going from v5 -> v6, v7
  • Logged In: YES

    The line "readAtomTypes getResourceAsStream" is actually
    not a complaint... but a remnant debug message...
    Moreover, I can edit the .jmol/jmol_atomtypes.txt file,
    restart Jmol and see the changes in the table...
    Could you give me the output of:
    java -Dcdk.debugging=true -jar jmol.jar | grep AtomType

    BTW, what about the history file? Is that a separate bug,
    or related to the atom types? Is it correct that the
    recent files list is not updated when Jmol is restarted
    and new files are opened? And what is the relation with
    the povray path?

  • Logged In: YES

    Sorry to be not precise enough. I meant changing atom properties
    from *within* jmol itself. This was possible in ver 5: the values
    could be changed and the color through a color chooser. The
    changes worked immediatly without having to restart jmol.

    In ver 5 the history file is updated for opening *any new* file
    whereas in ver 7 the history file is read with its recent file entries
    but not updated with new ones. On the other hand changing the
    povpray path when exporting /rendering *is updated* in the same
    history file (just confirmed it under win98, irix and aix).

  • Michael

    Logged In: YES


    Which characteristics are you particularly interested in
    changing *on-the-fly*?


  • Logged In: YES


    I'm a "graphics" man maintaining the visualization software here in our institution for our scientists and not
    using Jmol deeply for myself. Some scientists were accustomed to changing characteristics in ver 5. Had
    there been serious reasons to change this behaviour?


  • Michael

    Logged In: YES


    > Had there been serious reasons to change this behaviour?

    We are in the process of completely rewriting the graphics
    rendering in Jmol. As a result there have been a lot of
    changes in this area.

    They should look at the RasMol/Chime compatible scripting
    commands which are now implemented in Jmol. These commands
    give complete control over atom diameter, bond diameter, and
    colors ... on an object by object basis.

    Write me if you have more questions.


  • Michael

    Logged In: YES

    Dietrich ,

    > Some scientists were accustomed to changing
    characteristics in ver 5.

    I would be very interested in starting a dialog with your
    Jmol users. I would like to know what type of work they are
    using it for and what features they want. Please have them
    email me mth@mth.com


  • Logged In: YES

    Dietrich, I believe most things can now easily be addressed
    with custom scripts. Please reopen if you have need for a
    different way to address the customization.

    • status: open --> closed-out-of-date