[Bioperl-l] help on pdb

[ani]

Hey Ed,
Thanks alot for the reply. I was wondering how accurate these programs
are? I thought the PDB files have experimentaly determined secondary
structure prediction and will me more accurate. Or it is the other
way?
I am downloading DSSP and STRIDE and try your suggestion.
Best regards,
Ani



On Fri, 29 Oct 2004 12:04:29 -0700, Ed Green <ed at compbio.berkeley.edu> wrote:
> 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
> >
> >
>

--
______________________"The Answer Lies in Genome"______________________
Dr. Animesh Sharma
Visiting Scientist, Indian Statistical Institute
+91 33 25752910 / 2577-7695, 2577-8085 (Room No. 904)


-- 
______________________"The Answer Lies in Genome"______________________
Dr. Animesh Sharma
Visiting Scientist, Indian Statistical Institute
+91 33 25752910 / 2577-7695, 2577-8085 (Room No. 904)