[Bioperl-l] help on pdb

Ed Green ed at compbio.berkeley.edu
Fri Oct 29 15:04:29 EDT 2004

Dear Ani-
May I make a few suggestions?  You may want to extract the sequence 
based on their secondary structure labels by running a secondary 
structure calling program like STRIDE or DSSP on the PDB file first. 
There are bioperl modules for handling this output, which I wrote 
(Bio::Structure::SecStr::*).  This may be better for your purpose 
because the secondary structure annotations in the PDB files themselves 
are author contributed and are not based on a standard definition of 
secondary structure element characteristics.  On the other hand, this 
may not matter for you.

Also be aware that missing data (failure of ths structure solution to 
resolve atoms or residues) may yield false "breaks" in secondary structure.

Good luck!

Ed Green

ani wrote:
> I have installed Bioperl 1.4 on my windows system. Now I want to use it to
> read pdb file and extract the sequence base on their secondary structure
> label. I would also like to have the coordinate of the c-alpha of these
> residues.
> I was trying to read the PDB.pm file but couldnt get the exact methods to do
> what I want.
> (http://doc.bioperl.org/releases/bioperl-1.4/Bio/Structure/IO/pdb.html)
> A web pointer/reference will do.
> Regards,
> Ani

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