[BiO BB] FW: finding sequence helix/sheet in pdb

[Mathura, Venkatarajan S.]

 Thanks kiran.  I know I can do it with RASMOl/MOLMOL but I would like
to do it an very large scale. I mean the entire pdb  (just for proteins)
or atleast non-redundant structures.  Currently I am using the pdb
header HELIX  or SHEET information. The script looks for starting/ending
helix and sheet residue info, and reads out single letter seq for the
sec structure regions using the residue number and start/end info. I
have already done this for 2096 pdb files and was quiet successful. But
the script doesn't handle cases where the residue numbers were numbered
by 15A,16B etc  (particularly in case of mutation). I am looking for
someone who have already extracted all  helix sequences in the pdb (I
mean 12000 structures) or who have scripts that can better handle the
problem mentioned above.  I would like to stick to the secondary
structure information from the pdb header (as supplied by authors)
rather using other programs to write out sec structures from just
co-ordinates alone.

Any response will be appreciated,

Thanks,

venkat

> 
> Hello,
> 
>   Do anyone have a script or know of a source where
> I can obtain the
> sequences of helix/sheet
> from pdb file. Any help will be appreciated! 
> 
> Thanks,
> 
> Venkat  
> 
> 
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