-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 10 June 2004 12:35, Miguel wrote: > >> What .pdb model are you using? > > > > I'm using 1d66-pwz.pdb from > > http://molvis.sdsc.edu/dna/1d66-pwz.pdb > > or > > http://www2.uah.es/biomodel/pruebas/jmol/dna_jmol/1d66-pwz.pdb > > 1D66 seems to be a favorite of many people. In addition, I have no > credentials as a biochemist :-) > Therefore, it is with some reluctance/trepidation/self-conscious-fear that > I feel compelled to say ... > > 1D66.pdb is messed up.
Gert Vriend (here in Nijmegen) wrote software that checks PDB files: To see how much 1D66 is messed up ( including nuances), see: http://www.cmbi.kun.nl/cgi-bin/nonotes?PDBID=1D66 Which can be accessed from: http://www.cmbi.kun.nl/gv/pdbreport/ > The disoriented creature is [C]28 ... its forlorn partner is [G]11 ... go > see for yourself. The report mentions G11 related to "Buried unsatisfied hydrogen bond donors" and D11/C28 related to "Abnormally short interatomic distances". There is also a section on fliped side chains for amino acids, but apparently not for nucleic bases... Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAyF1hd9R8I9Yza6YRAoFwAJ9sWwGB1kNMVkz8EzwvlfLkEpRioACgi2Gh eZ/Lf4zjTfHzqritf7IuyTs= =+Tpb -----END PGP SIGNATURE----- ------------------------------------------------------- This SF.Net email is sponsored by: GNOME Foundation Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. GNOME Users and Developers European Conference, 28-30th June in Norway http://2004/guadec.org _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
