Bugs item #3463509, was opened at 2011-12-21 12:27 Message generated for change (Tracker Item Submitted) made by molusc2 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3463509&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: Scripting Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Paul Pillot (molusc2) Assigned to: Bob Hanson (hansonr) Summary: show smiles not always providing Z/E isomer information Initial Comment: Using scribmol, I drew but-2-ene (cis-conformation) in chemdoodle. The corresponding 3D molecule is created by Jmol. "show smiles" gives : C/C=CC when transfered to cactus for optimization, the resulting 3D file is in trans configuration (the 2D mol file shows a crossed double bond) Sometimes (I can't find a reproductible scenario), when I draw the same molecule directly in Jmol, the "show smiles" gives : C(/C)=C/C which leads to a correct optimization. In trans configuration, the results are quite similar : "show smiles" gives C(/C)=CC which leads to a crossed double bond with cactus, but provides a molecule in trans configuration (I suppose it is the default) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3463509&group_id=23629 ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
