#104 Lanthanide complexes as PDB - problems

v8
closed-fixed
Miguel
5
2004-05-26
2004-01-02
Nick Greeves
No

Certain X-ray stuctures as PDB files display well under
Chime but poorly under Jmol.
I have created a web page to demonstrate the problems
which range from incorrectly sizing the structure in the
frame, failing to display the central lanthanide ion, and
introducing spurious bonds to nearby lithium ions.

http://www.liv.ac.uk/Chemistry/jmol/test2.html

There is a wide variety of software that claims to export PDB
files but the resulting files are not all the same! It would be
useful if Jmol was as forgiving as possible.

This represents a significant problem for anyone seeking to
convert a Chime based site as every structure would require
careful individual checking.

Discussion

  • Michael
    Michael
    2004-01-02

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    It looks like you are using Jmol v8 ... the current official
    release of Jmol.

    If you are converting existing Chime applications, I strongly
    suggest that you switch to Jmol v10 ... currently in Beta test.

    Goto http://jmol.sf.net/betatest

    Jmol v10 has significantly enhanced .pdb support with an
    explicit goal of being a Chime replacement.

    It may still have troubles with these .pdb files, so please let
    me know how files work with v10.

    Miguel

     
  • Nick Greeves
    Nick Greeves
    2004-01-02

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    Indeed I was using Jmol v8 but switching to v10pre4 improves
    things tremendously (and the applet is so much smaller which is
    great for slower connections) - great job!

    The only PDB that still has any problems is the first one which fails
    to colour the atoms correctly - Barbie pink!! The freestanding
    application has the same problem.

    An unrelated query: Chime allowed "spin" to be set and the
    structure would turn forever which i liked for many of our
    examples. Can this be set in Jmol (and the speed controlled)?

    Nick

     
  • Michael
    Michael
    2004-01-03

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    Glad that v10 works better.

    The hot pink color was chosen to make it easily visible ...
    I guess it worked.

    When things show up in pink it is generally because the
    atomic symbol is not recognized.

    Please send me the file that is causing you trouble ...
    directly to mth@mth.com

    I am not a chemist ... a two sentence explanation of the
    molecule you are trying to work with would be helpful.

    Miguel

     
  • Michael
    Michael
    2004-01-29

    • assigned_to: nobody --> michaelthoward
     
  • Michael
    Michael
    2004-05-14

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    Nick,

    I would like to try to close this bug report ... again :-)

    Are the outstanding issues resolved with the current version
    of Jmol v10 pre ?

    Miguel

     
  • Michael
    Michael
    2004-05-14

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    ---------------------------- Original Message
    ---------------------------- Subject: Re: [ jmol-Bugs-869549
    ] Lanthanide complexes as PDB - problems From: "Nick
    Greeves" <ngreeves@liv.ac.uk>
    Date: Fri, May 14, 2004 21:12
    To: "Miguel Howard" <mth@mth.com>
    --------------------------------------------------------------------------

    Hi Miguel,

    Yes, this can safely be closed. It works well with our
    lanthanide structures now.

     
  • Michael
    Michael
    2004-05-14

    • status: open --> closed-fixed
     
  • Miguel
    Miguel
    2004-05-26

    • assigned_to: michaelthoward --> migueljmol