Bugs item #3604789, was opened at 2013-02-14 19:16 Message generated for change (Comment added) made by hansonr 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: Bob Hanson (hansonr) Date: 2013-02-15 10:51 Message: OK, I know what is going on. Sorry to inform you, but 12.2 was not doing what you thought it was. The command isosurface ID "isosurface1" vanderWaals 100% color "bgyor" range all map mep ignores all the cube data in the file (the command is not even trying to read the cube data, because the command does not specify that) and just uses the nuclear charges of the atoms for the "charges." Somewhere along the way I realized that was inappropriate and removed that option. On the other hand, isosurface ID "isosurface1" vanderWaals 100% color "bgyor" range all map "" gives a VDW surface with SOME coloration, but the data are extremely strange. With 13.1 I can use load http://dl.dropbox.com/u/12683952/jmol/L-proline_7_-0.570000.cube set drawhover isosurface color density "" and then check the points, and they are just ridiculous. Huge huge positive and negative numbers in very strange locations. Something is very wrong with that CUBE file. What else do you have that can display it? ---------------------------------------------------------------------- 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 ------------------------------------------------------------------------------ The Go Parallel Website, sponsored by Intel - in partnership with Geeknet, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials, tech docs, whitepapers, evaluation guides, and opinion stories. Check out the most recent posts - join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
