From: SourceForge.net <no...@so...> - 2010-02-26 21:16:32
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Bugs item #2959843, was opened at 2010-02-26 22:16 Message generated for change (Tracker Item Submitted) made by aherraez You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2959843&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: Open Resolution: None Priority: 5 Private: No Submitted By: Angel Herraez (aherraez) Assigned to: Nobody/Anonymous (nobody) Summary: water is not solvent Initial Comment: I was trying to update the definition of "solvent" and "water" and I found this in 11.9.25: This is the test file (XYZ format): ----------------- 3 some name O 0.6236923 -10.35712 -6.541425 T 1.089779 -9.90739 -5.792108 D 0.1222496 -9.632477 -6.993528 ----------------- and this is what Jmol says: $ select water 3 atoms selected # OK $ select solvent 0 atoms selected # BAD $ select ions 3 atoms selected # BAD, ions should be "solvent and not water" -classic meaning-, or at least the PO4 and SO4 group IDs The same happens with a plain O, H, H file -so it's not a problem with D or T ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2959843&group_id=23629 |
From: SourceForge.net <no...@so...> - 2010-02-27 15:19:27
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Bugs item #2959843, was opened at 2010-02-26 15:16 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2959843&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 >Resolution: Fixed Priority: 5 Private: No Submitted By: Angel Herraez (aherraez) Assigned to: Nobody/Anonymous (nobody) Summary: water is not solvent Initial Comment: I was trying to update the definition of "solvent" and "water" and I found this in 11.9.25: This is the test file (XYZ format): ----------------- 3 some name O 0.6236923 -10.35712 -6.541425 T 1.089779 -9.90739 -5.792108 D 0.1222496 -9.632477 -6.993528 ----------------- and this is what Jmol says: $ select water 3 atoms selected # OK $ select solvent 0 atoms selected # BAD $ select ions 3 atoms selected # BAD, ions should be "solvent and not water" -classic meaning-, or at least the PO4 and SO4 group IDs The same happens with a plain O, H, H file -so it's not a problem with D or T ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2010-02-27 09:19 Message: fixed for Jmol 11.8.19 and Jmol 11.9.31 sure enough. That's broken at least back to 11.6. select ions actually selects ALL ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2959843&group_id=23629 |
From: Angel H. <ang...@ua...> - 2010-02-27 17:02:50
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> >Status: Closed > >Resolution: Fixed > Summary: water is not solvent > >Comment By: Bob Hanson (hansonr) > Date: 2010-02-27 09:19 > > Message: > fixed for Jmol 11.8.19 and Jmol 11.9.31 > > sure enough. That's broken at least back to 11.6. > > select ions > > actually selects ALL Good. I still have a doubt lurking: If I understand correctly, apart from reading group IDs, Jmol interprets water molecules based on their chemical structure (as e.g. in xyz or mol files, with no group IDs). I think also important that "solvent" will include such water (not sure if it is doing so now, still haven't found the code where ID-less water is interpreted) |
From: Robert H. <ha...@st...> - 2010-02-27 18:36:17
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JmolConstants "@water _g>=" + GROUPID_WATER + " & _g<" + (GROUPID_WATER + 3) + ", oxygen & connected(2) & connected(2, hydrogen or deuterium or tritium), (hydrogen or deuterium or tritium) & connected(oxygen & connected(2) & connected(2, hydrogen or deuterium or tritium))", "@hoh water", Bob 2010/2/27 Angel Herráez <ang...@ua...> > > >Status: Closed > > >Resolution: Fixed > > Summary: water is not solvent > > > >Comment By: Bob Hanson (hansonr) > > Date: 2010-02-27 09:19 > > > > Message: > > fixed for Jmol 11.8.19 and Jmol 11.9.31 > > > > sure enough. That's broken at least back to 11.6. > > > > select ions > > > > actually selects ALL > > > Good. I still have a doubt lurking: > > If I understand correctly, apart from reading group IDs, Jmol interprets > water molecules > based on their chemical structure (as e.g. in xyz or mol files, with no > group IDs). > I think also important that "solvent" will include such water (not sure if > it is doing so now, still > haven't found the code where ID-less water is interpreted) > > > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 |