#417 cif read error

closed-fixed
Miguel
5
2008-02-07
2008-01-23
Anonymous
No

It's a bug. Jmol sees the "TITLE " line and assumes this is a PDB file. I will fix that, but for now you need to

load cif::filename.cif

to force reading as CIF format.

> Egon and Robert,
> I tried opening a variety of CIF files from the Database of Zeolite
> Structures:
>
> http://www.iza-structure.org/databases/
>
> but get the following error message with Jmol (version 11.4 RC1) shown in
> the enclosed pdf file. Please find enclosed a typical CIF file from the
> database for your consideration. For some reason the viewer DIAMOND -
> (Crystal and Molecular Structure Visualization - */
> /* Demonstration Version 3.1e) can visualize these
> structures. Does Jmol lack some additional features?
>
> Thanks in advance.
>
> Sincerely,
> Alex

Discussion

  • Nobody/Anonymous

    Logged In: NO

    that initial issue is fixed, but there is the additional issue that these files contain a nonstandard description of symmetry operations:

    _symmetry_equiv_pos_as_xyz
    ' +x +y +z '
    ' -x +y +z '
    ' +x -y 1/2+z '
    ' -x -y 1/2+z '
    ' -x -y -z '
    ' +x -y -z '
    ' -x +y 1/2-z '
    ' +x +y 1/2-z '

    that does not include commas between the operations. Jmol is expecting commas, and currently does not read these operations. I will look into fixing that even though it does not really constitute a bug.

    Bob Hanson

     
  • Bob Hanson

    Bob Hanson - 2008-02-07
    • status: open --> closed-fixed
     
  • Nobody/Anonymous

    I am experiencing possibly related errors: if I download a CIF from the IUCr's website,
    then upload to a Jmol tool (e.g. the IUCr's jmol toolkit), I get the 'unrecognzed fie format'
    message.

    This only occurs on LINUX and MAC (windows is OK -for a change!)

    However, if I remove the comment section from the start of the CIF (or just add a
    'dummy' data block before the comment section), Jmol has no problems
    recognizing it. There's nothing obvious in the 'offending' comment section (to me anyway).

    A further curiosity is that when I test the same CIFs using my 'localhost' server, everything is OK.

    I've been using Jmol 11.6.x - I havnt tested the development versions yet.

    You should be able to see this behaviour if you look at

    http://www.publcryst.co.uk/demos/jmol/sup_bug.php?issue=06&cifid=br2107

    (using Firefox on Linux or Mac - even if model loads first time, it probably wont if you reload)

    I'm not sure if this is a Jmol bug or a peculiarity of how the browser caches the CIF,
    or ...? (NB Opera on linux is OK)

    Anyway, I think its probably worth reporting just in case anyone else experiences
    problems with these CIFs

    Cheers

    simon@publcif.co.uk

     

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