Recent changes to bugs

#636 inconsistency between Jmol and JmolData

Bob Hanson — Sat, 10 Jan 2026 17:30:47 -0000

status: open --> closed

#636 inconsistency between Jmol and JmolData

Bob Hanson — Sat, 10 Jan 2026 17:28:56 -0000

Actually, both programs are showing this message. But it is not a meaningful message. It is just a warning that "variable" is not a property that can be set in an isosurface. It arises from my forgetting to take out some unused code in IsoExt.java. I've tracked down where it is coming from and removed that code. Thanks for spotting this.

inconsistency between Jmol and JmolData

John Terning — Fri, 09 Jan 2026 00:24:56 -0000

the following script runs in Jmol
load h3.RHO.140.cube
write h3.pdb
delete all
isosurface h3_140 cutoff 0.04 "h3.RHO.140.cube"
write OBJ h3_140.wrl
but in JmolData gives the error:
unassigned Isosurface + shape setProperty:variables:{var _deletedAtoms=Token[bitset(10/0xa) value=({0:2})][null index =2147483647 intValue=2147483647]}

inconsistency between Jmol and JmolData

John Terning — Fri, 09 Jan 2026 00:24:56 -0000

Ticket 636 has been modified: inconsistency between Jmol and JmolData
Edited By: Bob Hanson (hansonr)
Status updated: 'open' => 'closed'

Releases on Maven Central?

Egon Willighagen — Sun, 23 Nov 2025 13:51:16 -0000

Hi Bob, a few weeks ago I was asked about the Jmol binary release Maven Central (https://mvnrepository.com/artifact/net.sourceforge.jmol/jmol). Are you okay if I pick this up? I will likely have to write some patches, which would be nice after so many years.

#634 v14 vs. v16: Inconsistent orbials visualization from Molden file

Bob Hanson — Mon, 10 Nov 2025 23:31:57 -0000

Indeed. The presence of G orbitals causes the MO coefficient pointer to go awry.
This is fixed for Jmol 16.32.37/38. for a preview release Jmol.jar, see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/test/jmol-jar/

v14 vs. v16: Inconsistent orbials visualization from Molden file

Marco Foscato — Mon, 10 Nov 2025 13:49:59 -0000

Hi Jmol!

I experience an inconsistency in the visualization of molecular orbitals from an input file of Molden format. I hope I'll eventually get more details, but so far I was only able to track the issue down to the major version change: from v14 to v16.

Here is how to reproduce the problem with the attached input file:
1) open the attached file with v14.32.83 and v16.3.35 (I've tried also 16.3.33: same result as 16.3.35)
2) display any molecular orbital, for example, say "mo 8".
3) Now look at the results: v14 displays MO shapes that are consistent with Molden, but v16 displays different MOs shapes.

Perhaps, this is due to a different interpretation/assumption on the angular momentum of the basis?

Cheers,
Marco

#633 Unable to view FILE.37

Bob Hanson — Tue, 26 Aug 2025 23:31:04 -0000

The -2147483648 error is indicating that the file was found, but its format was different from what was expected. nbo files #37 are reading correctly for our test set. Please attach the file in a response to this message so we can see what might be the issue. Probably a simple fix.

Q: What is the source version of ORCA you are using? This might be something you will need to address with that group.

But first, let's find out exactly what the problem is.

#633 Unable to view FILE.37

Angel Herraez — Tue, 26 Aug 2025 18:27:00 -0000

Hello, Maureen
For this kind of problems, you should use the jmol-users email distribution list.
Anyway, it is hard to help unless you share the problematic file.

Unable to view FILE.37

Maureen Kitheka — Tue, 26 Aug 2025 18:08:54 -0000

Hi,

I'm trying to view FILE.37 generated using orca/nbo, but I'm unable to do so. I have a Jmol script, and with the same script, I can open FILE.32 to FILE.36 and FILE.38 to FILE.40. I even downloaded the latest version of Java, but I still get the same error message.

script ERROR: Error reading file at end of file
-2147483648
for file /Users/Desktop/test/FILE.37
type GenNBO
----line 1 command 1 of /Users/Desktop/test/mol.jmol:
load "FILE.37"<<<<
----line 1 command 1 of /Users/Desktop/test/mol.jmol:
script "mol.jmol"

Does anyone know how to fix this? Please advise.