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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
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