PALSSE: FAQ

http://prodata.swmed.edu/palsse/FAQ

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Q:

On Sat, Jun 03, 2006 at 08:52:58AM -0500, tozim@gmx.de wrote:
> Hello!
> 
> 
> 
> I would have a question to an example output line of a PALSSE file:
> 
> 
> 
> SHEET        5   SER   186  SER   189       4
> 
> 
> 
> This is a line from 1gcd. All sheets carry different numbers at the 
> 
> second position. At helices, this is a number for the helix, right? 
> 
> Because it\'s counted up from 1 to the maximal amount of helices in the
> 
> protein. But what about this second slot at sheets?
> 
> 
> 
> Excuse me for the question, I didn\'t find any explanation in your paper
> 
> or at the website and so I thought, I might ask you. 
> 
> 
> 
> Thank you and with best wishes, 
> 
> Tobias Zimmer
> --

A:

Hi Tobias,

Thanks for your question. This is the sheet ID for the sheet that the
strand belongs in (as mentioned in the PDB format). The number of sheets
is counted very simply by looping through every strand pair which link
at 3 residues or more (minimum strand length).

Even though our method splits individual strands, we do not (yet) split
sheets (collective splitting of multiple strands). So eg. all strands of
a sandwich might belong to the same sheet if even one unbroken strand
connects both sides. We believe this to be a tertiary structure
definition problem (and hence is not discussed in the paper).

The sheet ID helps but requires to be used with some caution.
(pairup_strands() in Element.py explains the strand pair calculation)

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