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
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: Closed >Resolution: Invalid 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: Miguel (migueljmol) Date: 2005-07-28 12:29 Message: Logged In: YES user_id=1050060 The GAMESS output file that you sent me contains atoms identified by 'CA', 'C', and '0'. 'CA' is recognized as calcium 'C' is recognized as carbon '0' is not recognized ... because the character in the GAMESS output file is the digit zero, not the alphabetic letter 'O' ... 0 != O (it is sad ... but also funny :-) I edited the file and changed appropriate characters from '0' -> 'O' ... Jmol loads it fine. I do not know anything about GAMESS or the process that was used to generate this file ... so I cannot tell you whether the problem is in GAMESS itself or was part of your input to GAMESS. Miguel ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2005-07-27 10:48 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 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 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1155968&group_id=23629 ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
