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From: Robert Hanson <hansonr@st...>  20100521 20:11:36

thanks  fixed. On Fri, May 21, 2010 at 2:16 PM, Nicolas Vervelle <nvervelle@...>wrote: > Hi, > > When running the unit tests, I have several exceptions for the crystal > reader : > > > java.lang.StringIndexOutOfBoundsException: String index out of range: 28 > at java.lang.String.substring(String.java:1935) > at > org.jmol.adapter.readers.xtal.CrystalReader.readGradient(CrystalReader.java:312) > at > org.jmol.adapter.readers.xtal.CrystalReader.checkLine(CrystalReader.java:237) > at > org.jmol.adapter.smarter.AtomSetCollectionReader.readAtomSetCollection(AtomSetCollectionReader.java:218) > at > org.jmol.adapter.smarter.AtomSetCollectionReader.readData(AtomSetCollectionReader.java:191) > at > org.jmol.adapter.smarter.Resolver.getAtomCollectionAndCloseReader(Resolver.java:263) > at > org.jmol.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollectionFromReader(SmarterJmolAdapter.java:78) > at > org.jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetCollectionFromReader(SmarterJmolAdapter.java:70) > > > junit.framework.AssertionFailedError: Error returned for > ..\Jmoldatafiles\crystal\alpha_quartz.out: Error reading file at line 893: > > String index out of range: 28 > for file alpha_quartz.out > type Crystal > > > > >  > > > _______________________________________________ > Jmoldevelopers mailing list > Jmoldevelopers@... > https://lists.sourceforge.net/lists/listinfo/jmoldevelopers > >  Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 5077863107 If nature does not answer first what we want, it is better to take what answer we get.  Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
From: Nicolas Vervelle <nvervelle@gm...>  20100521 19:17:21

Hi, When running the unit tests, I have several exceptions for the crystal reader : java.lang.StringIndexOutOfBoundsException: String index out of range: 28 at java.lang.String.substring(String.java:1935) at org.jmol.adapter.readers.xtal.CrystalReader.readGradient(CrystalReader.java:312) at org.jmol.adapter.readers.xtal.CrystalReader.checkLine(CrystalReader.java:237) at org.jmol.adapter.smarter.AtomSetCollectionReader.readAtomSetCollection(AtomSetCollectionReader.java:218) at org.jmol.adapter.smarter.AtomSetCollectionReader.readData(AtomSetCollectionReader.java:191) at org.jmol.adapter.smarter.Resolver.getAtomCollectionAndCloseReader(Resolver.java:263) at org.jmol.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollectionFromReader(SmarterJmolAdapter.java:78) at org.jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetCollectionFromReader(SmarterJmolAdapter.java:70) junit.framework.AssertionFailedError: Error returned for ..\Jmoldatafiles\crystal\alpha_quartz.out: Error reading file at line 893: String index out of range: 28 for file alpha_quartz.out type Crystal 
From: SourceForge.net <noreply@so...>  20100521 15:45:48

Bugs item #3005028, was opened at 20100520 20:29 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&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: User interface Group: None >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Miguel (migueljmol) Summary: loss of feature in rev 12 Initial Comment: This could have happened a long time ago since I haven't been keeping my version up to date. But in the 11.x versions whenever you read a g03 output file with different input and standard orientations in a geometry optimization calculation, the AtomSetChooser would be able to show the same kind of orientations in the same 'folder'. The frequency calculation results would be in their own folder again. This makes it a lot easier to animate optimizations and stay within one set of orientations (so you don't get the flipping of the molecules). Between 11.6.x or so and 12 the reader has been modified so much that I can't really figure out any more how to set this up (even though I initially implemented it a long time ago). Sigh....  >Comment By: Bob Hanson (hansonr) Date: 20100521 10:45 Message: OK, that's fixed  just had two lines switched order in ModelLoader. Thanks, Bob  Comment By: Bob Hanson (hansonr) Date: 20100521 10:35 Message: duh. I see it now  Jmol!  Comment By: Bob Hanson (hansonr) Date: 20100521 10:35 Message: duh. I see it now  Jmol!  Comment By: Bob Hanson (hansonr) Date: 20100521 10:32 Message: Rene, it's the .PATH property: atomSetCollection.setAtomSetProperty(SmarterJmolAdapter.PATH_KEY, "Calculation "+calculationNumber+ (scanPoint>=0?(SmarterJmolAdapter.PATH_SEPARATOR+"Scan Point "+scanPoint):"")+ SmarterJmolAdapter.PATH_SEPARATOR+path); as far as I know, that should still work. For example, I see for one of the test files: auxiliaryinfo.properties.PATH_SEPARATOR ";" auxiliaryinfo.properties.PATH_KEY ".PATH" modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[4].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[5].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[6].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[7].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[8].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[9].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[10].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[11].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[12].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[13].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" and for another: modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;Input" modelinfo.models[4].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[5].modelProperties..PATH "Calculation 1;Input" modelinfo.models[6].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[7].modelProperties..PATH "Calculation 1;Input" modelinfo.models[8].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[9].modelProperties..PATH "Calculation 1;Input" modelinfo.models[10].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[11].modelProperties..PATH "Calculation 2;Input" modelinfo.models[12].modelProperties..PATH "Calculation 2;Standard" modelinfo.models[13].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[15].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" These are exactly the same properties that are shown using Jmol 10.9, so maybe it's just how you are extracting them. What are you using to view this hierarchy? Bob maybe there is  You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&group_id=23629 
From: SourceForge.net <noreply@so...>  20100521 15:35:26

Bugs item #3005028, was opened at 20100520 20:29 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&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: User interface Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Miguel (migueljmol) Summary: loss of feature in rev 12 Initial Comment: This could have happened a long time ago since I haven't been keeping my version up to date. But in the 11.x versions whenever you read a g03 output file with different input and standard orientations in a geometry optimization calculation, the AtomSetChooser would be able to show the same kind of orientations in the same 'folder'. The frequency calculation results would be in their own folder again. This makes it a lot easier to animate optimizations and stay within one set of orientations (so you don't get the flipping of the molecules). Between 11.6.x or so and 12 the reader has been modified so much that I can't really figure out any more how to set this up (even though I initially implemented it a long time ago). Sigh....  >Comment By: Bob Hanson (hansonr) Date: 20100521 10:35 Message: duh. I see it now  Jmol!  Comment By: Bob Hanson (hansonr) Date: 20100521 10:35 Message: duh. I see it now  Jmol!  Comment By: Bob Hanson (hansonr) Date: 20100521 10:32 Message: Rene, it's the .PATH property: atomSetCollection.setAtomSetProperty(SmarterJmolAdapter.PATH_KEY, "Calculation "+calculationNumber+ (scanPoint>=0?(SmarterJmolAdapter.PATH_SEPARATOR+"Scan Point "+scanPoint):"")+ SmarterJmolAdapter.PATH_SEPARATOR+path); as far as I know, that should still work. For example, I see for one of the test files: auxiliaryinfo.properties.PATH_SEPARATOR ";" auxiliaryinfo.properties.PATH_KEY ".PATH" modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[4].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[5].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[6].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[7].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[8].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[9].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[10].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[11].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[12].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[13].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" and for another: modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;Input" modelinfo.models[4].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[5].modelProperties..PATH "Calculation 1;Input" modelinfo.models[6].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[7].modelProperties..PATH "Calculation 1;Input" modelinfo.models[8].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[9].modelProperties..PATH "Calculation 1;Input" modelinfo.models[10].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[11].modelProperties..PATH "Calculation 2;Input" modelinfo.models[12].modelProperties..PATH "Calculation 2;Standard" modelinfo.models[13].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[15].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" These are exactly the same properties that are shown using Jmol 10.9, so maybe it's just how you are extracting them. What are you using to view this hierarchy? Bob maybe there is  You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&group_id=23629 
From: SourceForge.net <noreply@so...>  20100521 15:35:25

Bugs item #3005028, was opened at 20100520 20:29 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&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: User interface Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Miguel (migueljmol) Summary: loss of feature in rev 12 Initial Comment: This could have happened a long time ago since I haven't been keeping my version up to date. But in the 11.x versions whenever you read a g03 output file with different input and standard orientations in a geometry optimization calculation, the AtomSetChooser would be able to show the same kind of orientations in the same 'folder'. The frequency calculation results would be in their own folder again. This makes it a lot easier to animate optimizations and stay within one set of orientations (so you don't get the flipping of the molecules). Between 11.6.x or so and 12 the reader has been modified so much that I can't really figure out any more how to set this up (even though I initially implemented it a long time ago). Sigh....  >Comment By: Bob Hanson (hansonr) Date: 20100521 10:35 Message: duh. I see it now  Jmol!  Comment By: Bob Hanson (hansonr) Date: 20100521 10:32 Message: Rene, it's the .PATH property: atomSetCollection.setAtomSetProperty(SmarterJmolAdapter.PATH_KEY, "Calculation "+calculationNumber+ (scanPoint>=0?(SmarterJmolAdapter.PATH_SEPARATOR+"Scan Point "+scanPoint):"")+ SmarterJmolAdapter.PATH_SEPARATOR+path); as far as I know, that should still work. For example, I see for one of the test files: auxiliaryinfo.properties.PATH_SEPARATOR ";" auxiliaryinfo.properties.PATH_KEY ".PATH" modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[4].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[5].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[6].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[7].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[8].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[9].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[10].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[11].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[12].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[13].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" and for another: modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;Input" modelinfo.models[4].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[5].modelProperties..PATH "Calculation 1;Input" modelinfo.models[6].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[7].modelProperties..PATH "Calculation 1;Input" modelinfo.models[8].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[9].modelProperties..PATH "Calculation 1;Input" modelinfo.models[10].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[11].modelProperties..PATH "Calculation 2;Input" modelinfo.models[12].modelProperties..PATH "Calculation 2;Standard" modelinfo.models[13].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[15].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" These are exactly the same properties that are shown using Jmol 10.9, so maybe it's just how you are extracting them. What are you using to view this hierarchy? Bob maybe there is  You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&group_id=23629 
From: SourceForge.net <noreply@so...>  20100521 15:32:13

Bugs item #3005028, was opened at 20100520 20:29 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&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: User interface Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Miguel (migueljmol) Summary: loss of feature in rev 12 Initial Comment: This could have happened a long time ago since I haven't been keeping my version up to date. But in the 11.x versions whenever you read a g03 output file with different input and standard orientations in a geometry optimization calculation, the AtomSetChooser would be able to show the same kind of orientations in the same 'folder'. The frequency calculation results would be in their own folder again. This makes it a lot easier to animate optimizations and stay within one set of orientations (so you don't get the flipping of the molecules). Between 11.6.x or so and 12 the reader has been modified so much that I can't really figure out any more how to set this up (even though I initially implemented it a long time ago). Sigh....  >Comment By: Bob Hanson (hansonr) Date: 20100521 10:32 Message: Rene, it's the .PATH property: atomSetCollection.setAtomSetProperty(SmarterJmolAdapter.PATH_KEY, "Calculation "+calculationNumber+ (scanPoint>=0?(SmarterJmolAdapter.PATH_SEPARATOR+"Scan Point "+scanPoint):"")+ SmarterJmolAdapter.PATH_SEPARATOR+path); as far as I know, that should still work. For example, I see for one of the test files: auxiliaryinfo.properties.PATH_SEPARATOR ";" auxiliaryinfo.properties.PATH_KEY ".PATH" modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[4].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[5].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[6].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[7].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[8].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[9].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[10].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[11].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[12].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[13].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 1;FrequenciesFrequencies" and for another: modelinfo.models[1].modelProperties..PATH "Calculation 1;Input" modelinfo.models[2].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[3].modelProperties..PATH "Calculation 1;Input" modelinfo.models[4].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[5].modelProperties..PATH "Calculation 1;Input" modelinfo.models[6].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[7].modelProperties..PATH "Calculation 1;Input" modelinfo.models[8].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[9].modelProperties..PATH "Calculation 1;Input" modelinfo.models[10].modelProperties..PATH "Calculation 1;Standard" modelinfo.models[11].modelProperties..PATH "Calculation 2;Input" modelinfo.models[12].modelProperties..PATH "Calculation 2;Standard" modelinfo.models[13].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[14].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" modelinfo.models[15].modelProperties..PATH "Calculation 2;FrequenciesFrequencies" These are exactly the same properties that are shown using Jmol 10.9, so maybe it's just how you are extracting them. What are you using to view this hierarchy? Bob maybe there is  You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&group_id=23629 
From: Robert Hanson <hansonr@st...>  20100521 15:05:22

should read all my messages.... Right, that's what I understand. His position is that there is no way of using the code he has, so he would have to start from scratch, and that is not very appealing or possible within his time allowances. On Fri, May 21, 2010 at 10:03 AM, Robert Hanson <hansonr@...> wrote: > Not according to Peter, but maybe he's going to surprise us. > > 2010/5/21 Angel Herráez <angel.herraez@...> > > I've just found (from reading his recent paper in J.Cheminformatics) >> that Peter Ertl is working on an opensource javascriptbased >> equivalent of JME. Might be a good complement for Jmol. >> >> >> >> >>  >> >> _______________________________________________ >> Jmoldevelopers mailing list >> Jmoldevelopers@... >> https://lists.sourceforge.net/lists/listinfo/jmoldevelopers >> > > > >  > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 5077863107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > >  Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >  Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 5077863107 If nature does not answer first what we want, it is better to take what answer we get.  Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
From: Robert Hanson <hansonr@st...>  20100521 15:04:04

Not according to Peter, but maybe he's going to surprise us. 2010/5/21 Angel Herráez <angel.herraez@...> > I've just found (from reading his recent paper in J.Cheminformatics) > that Peter Ertl is working on an opensource javascriptbased > equivalent of JME. Might be a good complement for Jmol. > > > > >  > > _______________________________________________ > Jmoldevelopers mailing list > Jmoldevelopers@... > https://lists.sourceforge.net/lists/listinfo/jmoldevelopers >  Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 5077863107 If nature does not answer first what we want, it is better to take what answer we get.  Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 
From: Angel Herráez <angel.herraez@ua...>  20100521 13:21:31

I just received news from Peter Ertl. The JME2 development is currently stalled with no known date for resuming it. ;( El 21 May 2010 a las 10:39, Angel Herráez escribió: > I've just found (from reading his recent paper in J.Cheminformatics) > that Peter Ertl is working on an opensource javascriptbased > equivalent of JME. Might be a good complement for Jmol. 
From: Angel Herráez <angel.herraez@ua...>  20100521 08:39:36

I've just found (from reading his recent paper in J.Cheminformatics) that Peter Ertl is working on an opensource javascriptbased equivalent of JME. Might be a good complement for Jmol. 
From: SourceForge.net <noreply@so...>  20100521 01:29:28

Bugs item #3005028, was opened at 20100520 20:29 Message generated for change (Tracker Item Submitted) made by rkanters You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&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: User interface Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Miguel (migueljmol) Summary: loss of feature in rev 12 Initial Comment: This could have happened a long time ago since I haven't been keeping my version up to date. But in the 11.x versions whenever you read a g03 output file with different input and standard orientations in a geometry optimization calculation, the AtomSetChooser would be able to show the same kind of orientations in the same 'folder'. The frequency calculation results would be in their own folder again. This makes it a lot easier to animate optimizations and stay within one set of orientations (so you don't get the flipping of the molecules). Between 11.6.x or so and 12 the reader has been modified so much that I can't really figure out any more how to set this up (even though I initially implemented it a long time ago). Sigh....  You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3005028&group_id=23629 