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
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Category: File Input/Output Group: None Status: Open Resolution: Invalid 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: 2013-02-18 06:18 Message: It's reading the file. In the isosurface command, since we have load xxx.cube when we use "" it is the same as "the current file loaded" which is the cube file. ---------------------------------------------------------------------- Comment By: Martin Olveyra (molv) Date: 2013-02-15 17:36 Message: Well, actually i see that the cube file is really wrong. With the command you wrote below isosurface ID "isosurface1" vanderWaals 100% color "bgyor" range all map mep "" i got the same result as when i use the isosurface command with the .cube file as input, so in fact seems it did not read anything from that file, and it is calculating some mep from some internal jmol means. May be there is something to fix after all, like avoid to generate the isosurface if the cube file does not contains valid data. ---------------------------------------------------------------------- Comment By: Martin Olveyra (molv) Date: 2013-02-15 16:45 Message: «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." » Oh... that explains many things. I was anyway using the old version since few time ago (comes with ubuntu), i am quite new to jmol, and just decided to upgrade to version 13 because i had many problems with applets with the version 12. «Somewhere along the way I realized that was inappropriate and removed that option. » Yeah, now that i understand the problem, i think that was a good measure, it avoids confusions in the future. Now I learned to load the cube data with the isosurface command, something that i did not know it was the correct way, that is why i raised the ticket in first place. Sorry for the mistake. So then i will close this ticket as invalid. About the strange values in the cube data file, i will investigate more, may be it is a problem with obprobe, but seems it does not affect the charge near the atom in order to compute the electrostatic potential. I will anyway search for another application that generates charges and compare. Thanks very much for the help! ---------------------------------------------------------------------- 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. 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