-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Mark,
I was tought to always check the outcome of automated secondary structure assignment, because it is defined by hydrogren bondings, not by what some software thinks. DSSP is certainly very good, but always worth comparing the boundaries with your own experience/ opinion.Maybe the authors of the mentioned PDB entries did exactly this - and fortunately, as has already been pointed out, the PDB do not overwrite the authors' opinion. Cheers, Tim On 07/25/12 22:55, Dr. Mark Mayer wrote: > I've recently noticed that the Helix and Sheet records in PDB > entries differ from those generated by DSSP and would like to ask > if anyone can explain how the PDB makes the assignments. Until now > I'd always assumed that the PDB and DSSP records were the same. > > As an example I've listed a few lines from 2V3U.pdb. There are > similar difference in both helix lengths and start/stop positions > that occur in 9 other entries I've looked at. > > 2V3U.pdb HELIX 1 1 GLY A 31 GLY A 45 1 > 15 HELIX 2 2 ASN A 68 PHE A 76 1 > 9 HELIX 3 3 THR A 89 ASN A 94 1 > 6 > > and for the same structure the DSSP entry from the CMBI data base > http://swift.cmbi.ru.nl/gv/dssp/ > > REMARK 1 secondary structure assigned by dssp HELIX 1 1 PHE > A 32 LEU A 44 1 13 HELIX 2 > 2 GLY A 69 VAL A 75 1 7 > HELIX 3 3 PRO A 90 GLU A 93 1 > 4 > > Its not a big deal, but makes comparing secondary structures a bit > more difficult. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQEOnOUxlJ7aRr7hoRAitSAKCVAsywkgfA5nWOxPjwivfgI6Hn7gCgkR3Y knXIwk7eN5cAc/NyjBunjFE= =MH89 -----END PGP SIGNATURE-----
