Al Wang wrote:
>> Hi,
>> Does anyone know what's a good way to take a Brookhaven PDB file, extract
> the sequence information, and save it in SwissPROT format? If it can
> also extract the secondary structure features, even better.
>
I'd just like to add a comment which might be relevant in this case: PDB
residue numbering is, at times, non-consecutive, or may contain
non-numeric characters (e.g. 31A). This may cause problems if somehow
you wish to later correlate your sequence file with the PDB file.
I recommend using DSSP, and then running a script on the resulting DSSP
file. That way you preserve PDB residue numbering, consecutive
numbering, and 2ndary structure.
About DSSP:
http://www.sander.embl-heidelberg.de/dssp/
Iddo
--
Iddo Friedberg
Phone: (972)-2-6758647
email: idoerg at cc.huji.ac.il
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