PDB -> SwissPROT conversion?

Paul Davis Paul at pdchem.demon.co.uk
Sat Jun 6 04:16:29 EST 1998


In article <bpmurray*STUFFER*-0506982020480001 at macmac-2.ucsf.edu>
           bpmurray*STUFFER*@socrates.ucsf.edu "Bernard Murray" writes:

> 
> Similarly, you can load the structure into RasMol and then type
> "show sequence" on the command line to have the sequence displayed
> (three letter format, not SwissProt) and you can then cut'n'paste
> to your heart's content.  Alas, I don't think there's an easy
> way to grap the secondary structrure assignments - you'll need a
> standalone version of the embedded DSSP algorithm.
> 

Try this on the RasMol command line:-

          structure
          save molscript <filename>
          
The first command uses RasMol's embedded DSSP algorithm to assign
secondary structure, overriding any HELIX and SHEET records in the
original PDB file.

The second command writes an input file for the MolScript program,
containing the secondary structure assignments.

>    Personally I echo a previous post to the effect that it is
> much easier to use links to the appropriate protein database.
> I believe the Brookhaven WWW site has hot links from their PDB
> entries to GenBank/SwissProt or whatever and NCBI's ENTREZ browser
> links the 3D structures to sequence files.  Many protein sequence
> files now seem to incorporate PDB-derived secondary structural
> information in their remarks.  

This is true; however I have been caught out once or twice in the
past when using the HELIX and STRAND Feature Tables in SWISS-PROT.
Just occasionally I have found them to contain inaccuracies, and
so I would recommend checking them yourself.


> Of course, you don't have this
> luxury if this is a novel PDB file.
>      When playing with PDB files generated by CHARMM I have used
> AWK scripts to extract the residue names from the PDB file lines
> containing the C-alpha (CA) atoms and then to convert three letters
> to one letter.  However, as pointed out in previous posts, most
> automatic methods are fooled by multiple chains or gaps so manual
> intervention is almost always needed.
>      Good luck,
>           Bernard

-Paul
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Paul Davis                                   paul at pdchem.demon.co.uk





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