#545 Cannot load MEP data from .cube file with last version

v10
closed-invalid
Bob Hanson
5
2014-03-07
2013-02-15
Martin Olveyra
No

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).

Discussion

  • Bob Hanson
    Bob Hanson
    2013-02-15

    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?

     
  • Martin Olveyra
    Martin Olveyra
    2013-02-15

    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

     
  • Martin Olveyra
    Martin Olveyra
    2013-02-15

    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?

     
  • Martin Olveyra
    Martin Olveyra
    2013-02-15

    a correction: the jmol version which i tested and works ok with this file is 12.2.2

     
  • Bob Hanson
    Bob Hanson
    2013-02-15

    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?

     
  • Martin Olveyra
    Martin Olveyra
    2013-02-16

    • status: open --> open-invalid
     
  • Martin Olveyra
    Martin Olveyra
    2013-02-16

    «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!

     
  • Martin Olveyra
    Martin Olveyra
    2013-02-16

    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.

     
  • Bob Hanson
    Bob Hanson
    2013-02-18

    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.

     
  • Bob Hanson
    Bob Hanson
    2014-03-07

    • status: open-invalid --> closed-invalid
    • Group: --> v10