[Bioperl-l] help on pdb
ed at compbio.berkeley.edu
Fri Oct 29 15:04:29 EDT 2004
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.
> 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
> I was trying to read the PDB.pm file but couldnt get the exact methods to do
> what I want.
> A web pointer/reference will do.
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