Bugs item #1155968, was opened at 2005-03-03 08:15 Message generated for change (Comment added) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. 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 [EMAIL PROTECTED] ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2005-07-27 07:48 Message: Logged In: NO Jmol v.10.00.24 now correctly identifies de Calcium atoms, but the oxygens are still shown as Xx atoms. Thanx for your attention. Victor M. Rosas Garcia [EMAIL PROTECTED] ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2005-03-03 08:53 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 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629 ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
