Question: Need Help With A Perl Code. A Total Newbie!
gravatar for puranikedsunil
6.3 years ago by
puranikedsunil0 wrote:

Hey guys, I am working on PDB files and i am using this perl module called parse pdb along with perl to extract some information, I have the secondary structure information with me, that is the helix and the loop rows in the pdb file, for example this is one line what i have extracted,

**SHEET   10   A10 ARG A 215  TYR A 220  1  N  MET A 219   O  SER A 187

However this gives me only the beginning and the terminal residues and their residue numbers, I want to extract all the residues in the secondary structures in multiple files, could someone provide me some insight on how to approach this, I have been digging for information for a long time now, have not found anything related to this online. Help would be really appreciated . Thank you

structure secondary • 1.7k views
ADD COMMENTlink modified 6.3 years ago by Woa2.7k • written 6.3 years ago by puranikedsunil0

Can't you just use the AA sequence in FASTA format?

ADD REPLYlink written 6.3 years ago by Michael Dondrup46k

I am not familiar with parse pdb module, but maybe if you show me input files and information about what you want to do with them, I will be able to help you.

ADD REPLYlink written 6.3 years ago by Biomonika (Noolean)3.0k
gravatar for Woa
6.3 years ago by
United States
Woa2.7k wrote:

Which PDB parsing module you're using?

You may find something useful HERE

ADD COMMENTlink written 6.3 years ago by Woa2.7k
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