Feature Requests item #1003898, was opened at 2004-08-05 07:11 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1003898&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: None Group: None >Status: Closed Priority: 5 Submitted By: Rene Kanters (rkanters) Assigned to: Nobody/Anonymous (nobody) Summary: dummy atoms Initial Comment: Hi, I am using JMol to look at Gaussian 03 output and wanted to know whether in a future version JMol will also show dummy atoms. Since I am using z-matrix optimizations, several of the angles that are important to me are defined using a dummy atom. It looks like JMol uses the standard orientation to parse for the multiple structures in a log file, which has the dummy atoms stripped. If it were to look for the "Z-Matrix orientation:" it would find the cartesian coordinates of all the atoms. The added advantage of using the Z-Matrix orientation is that it will also not flip my molecule around (which the standard orientation sometimes does). Thanks, Rene ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-08-22 18:42 Message: Logged In: YES user_id=1082841 no plans for this. ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-10-08 06:16 Message: Logged In: YES user_id=1050060 I am quite sure that we will be able to add this in a future version. Please attach a file of a small molecule that demonstrates the problem. Post a message which explains which are the 'dummy' atoms and how they are used. ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-08-05 08:43 Message: Logged In: YES user_id=1050060 Rene, I will be glad to work with you on this, but I will need your assistance ... I am not a chemist. Q: In 25 words or less, what is a dummy atom? Q: How should it be represented graphically in Jmol? I will take a look at some gaussian output and see if I can figure out what you mean by "z-matrix orientation". Even better, send me an email ([EMAIL PROTECTED]) with a gaussian 03 attachment that that contains a very small molecule that includes a 'dummy atom'. Miguel ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1003898&group_id=23629 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
