[ghemical-users] Ghemical freezes

thassine at messi.uku.fi thassine at messi.uku.fi
Fri Feb 22 05:02:27 EST 2008

Quoting David  Stephenson <David.Stephenson at sta.uwi.edu>:

> Dear Tommi,
> I am using ghemical 2.1 on windows XP.
> I think I'm beginning to see what the problem is.

Ok, great!

> If I open a selection window (say select element),and forget to cancel
> the window before drawing, the selection window minimizes, but stays as
> the active window. So the main window will not respond. I will see if
> that is the only problem.

Yes, originally the idea was that the element dialog and the bondtype dialog
would block access to the rest of the interface, requiring some selection
before the user can get back to other operations. It is unfortunate if this is
not working well in the version you are using.

> BTW the "save" option is also very difficult to use, as it does not come
> up from the "file tab", but on a right click.

Yes, this is not user-friendly ; I'll try to fix it in the next versions.

> I am at the moment trying to draw the Zwitter ion form of EDTA and that
> is giving some problems with the insertion of hydrogens. Also the
> Oxygens of the COO- group have changed colour - is that normal.

The "add hydrogens" operation cannot always work 100% correclty ; it is intended
as a useful "helper" tool but you should always check whether it did the right

If you try to run calculations and some atoms change colour it means that the
molecular mechanics force field did not find matching atom types for those
atoms and some default parameters have been used for those atoms. I'm trying to
improve this so that an error report would appear in the text log window.



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