[BiO BB] Re: [ssml] (no subject)

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Wed Dec 8 20:55:13 EST 2004

Hello Manisha!

Several groups have done semi-automatic and manual ATOM to SEQRES
mappings. I only know about two mappings in any detail.

One is done by the MSD in their relational database. If you ask the people
at the MSD they will give you their mapping table as a tab delimeted dump
(I think it is called the swissprot table) which includes ATOM, SEQRES and
SWISSPROT residue numbering, and the usual PDB residue identifiers

The other mapping is done by SCOP and is maintained by ASTRAL in the easy
to parse 'RAF' files. The RAF format gives the same information as above,
and is manually curated (and they maintain a list of edits which
unfortunatly the MSD don't).

Sadly the current version of SCOP is quite old, and hence the RAF files
for the current version are also old. Perhaps if you ask the people at
astral they can give you a 'beta' release.

If you like I can send you my RAF parser which creates a nice tab
delimited format, but actually the files are trivial to parse, or the tab
delimited file from MSD is just as good.

Let me know how you get on,
All the best,

On Wed, 8 Dec 2004, Goel, Manisha wrote:

>Dear All,
>I have been using protein sequences of proteins with known structures
>(PDB databse) derived from the SEQRES records. 
>But now that I need to run either DSSP or STRIDE on them.. I cannot map
>the secondary structure back to the sequence alignments because the
>SEQRES and ATOMS records do not agree on the residue number id.
>So a residue numbered as 278 in SEQRES record is listed as 268 in the
>ATOMS record, messing up my alignments (I was using this numbering to
>map the secondary structure on to the sequence)
>I have come across quite a bit of discussion in some mailing lists about
>the need & proposed methods of modification of the PDB files, so that
>they can be made consistent.
>BUT .. 
>Meanwhile can somebody suggest a method or resource .. which could
>either fix this dicrepency or maybe a round about way of taking care of
>I guess with people working with stuctural/sequence mapping so often,
>some such fix would have definetly been devised by somebody.
>I just want to be able to modify the residue numbers in the ATOMS record
>to match the SEQRES records or something to that effect. CIF does not
>work because it does not segregate by chain numbers/id.
>Thanks for any input,

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