[Jmol-developers] [ jmol-Bugs-1155968 ] Jmol gets confused by GAMESS output file

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Bugs item #1155968, was opened at 2005-03-03 11:15
Message generated for change (Comment added) made by migueljmol
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629

Category: File Input/Output
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Miguel (migueljmol)
Summary: Jmol gets confused by GAMESS output file

Initial Comment:
When opening the attached file with Jmol v.10.00.11, no
bonds are shown, the oxygens are shown as Xx atoms
(small and pink instead of medium red atoms) and
calcium atoms are mistaken as carbons.
The Jmol console does not report any errors.

Jmol v.9 identifies correctly all the atoms and bonds.

The attached output file is the smallest case I found
where this bug shows up.  Maybe it has something to do
with the high symmetry (Td group) of the molecule?

The attached GAMESS output file should NOT be
redistributed.  I am submitting it for debugging only.

Thanx for your attention.

Victor M. Rosas Garcia
qui...@ya...


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>Comment By: Miguel (migueljmol)
Date: 2005-03-03 11:53

Message:
Logged In: YES 
user_id=1050060

The GAMESS reader was completely rewritten between Jmol v9
and Jmol v10 ... like all the other code. 

Probably some type of column-alignment problem ... hence Ca
-> C ... but that does not explain the problem with O

There are no bonds because the element Xx (unknown) does not
bond. 

There was no attached file ... can you send it to me off-list?

Miguel


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