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[Jmol-developers] [ jmol-Bugs-3604789 ] Cannot load MEP data from .cube file with last version
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From: SourceForge.net <no...@so...> - 2013-02-15 05:15:06
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Bugs item #3604789, was opened at 2013-02-14 19:16 Message generated for change (Comment added) made by molv You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3604789&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: Open Resolution: None Priority: 5 Private: No Submitted By: Martin Olveyra (molv) Assigned to: Bob Hanson (hansonr) Summary: Cannot load MEP data from .cube file with last version Initial Comment: Example: http://dl.dropbox.com/u/12683952/jmol/L-proline_7_-0.570000.cube Open this file with the last version of jmol (13.0.10, i saw that there is a 13.0.12 but don't see fix in change log), and in console type: $ isosurface ID "isosurface1" vanderWaals 100% color "bgyor" range all mep error message: script ERROR: No partial charges were read from the file; Jmol needs these to render the MEP data. i don't have problem with my previous version of jmol (version 10). ---------------------------------------------------------------------- >Comment By: Martin Olveyra (molv) Date: 2013-02-14 21:15 Message: a correction: the jmol version which i tested and works ok with this file is 12.2.2 ---------------------------------------------------------------------- Comment By: Martin Olveyra (molv) Date: 2013-02-14 21:02 Message: I don't know how it is supposed to look a cube file with charge data because don't know the format file specs, but considering that the file was generated by obprobe, which in fact its purpose is to generate charge data, i don't know what to answer to you when you say that the file does not have charge data. Also, considering that jmol 10 can read that data and show the electrostatic potential map over the given isosurface :) may be some different format versions? ---------------------------------------------------------------------- Comment By: Martin Olveyra (molv) Date: 2013-02-14 20:55 Message: More details: The file was generated with obprobe over the .mol file http://dl.dropbox.com/u/12683952/jmol/L-proline.mol using the command obprobe 7 -0.57 L-proline.mol which generates a cube file with charge data that i was able to read in jmol version 10 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2013-02-14 20:25 Message: That's quite curious, because Jmol to my knowledge has never automatically read any cube data as MEP data. "version 10" covers a lot of territory, though, so I suppose it's possible. MEP data requires charges, and this file has no charge data. I can map it to VDW, but not using MEP, just using "", and it is not very clear that is showing me an electron potential. The numbers are huge, even quite far from the molecule -- 64.56, 1991.7. What could this be? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3604789&group_id=23629 |