[BioPython] Extracting residue list from PDB

[Gad Abraham]

On Sat, Oct 29, 2005 at 12:45:38AM -0400, Boris Steipe wrote:
> SEQRES and ATOM records have different semantics: the SEQRES is what  
> the crystallographer puts into the experiment, the ATOM records is  
> what she sees. Presumably you have covalent chain-breaks between  
> residues, or parts of the polypeptide chain were not traceable in  
> electron density and were omitted.
> 
> So even though they numbers are inconsistent, they are both right.
> 
> A related issue may be what the natural protein sequence is, as  
> opposed to the perhaps truncated molecule in the crystal (presumably  
> you are not interested in the propensity of fragments to crystallize,  
> but in some biological property), or what the translated sequence is,  
> that may have been posttranslationally processed, or even what the  
> gene sequence is, that may have been translated with e.g.  
> selenocysteine, etc. etc.
> 
> So, (as usual) "the way to go" is determined by where you want to go to.

Like everyone else, I'm trying to predict structure from sequence. So
I'm interested in the true sequence of the chain, and what the
corresponding tertiary structure is. So it seems to me that the SEQRES
entries are the more correct sequence to use, because the ATOM entries
are a function of the latter (convoluted through experiments), not the
other way round.

Thanks,
Gad

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gabraham at cs.rmit.edu.au
http://yallara.cs.rmit.edu.au/~gabraham
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