[BiO BB] how to calculate the atom distance between antigen and antibody

Mike Marchywka marchywka at hotmail.com
Fri Jul 18 05:49:15 EDT 2008



> Date: Wed, 16 Jul 2008 15:20:08 -0500
> From: me.lixue at gmail.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] how to calculate the atom distance between antigen and antibody
>
> Thank you guys for replying my email.
>
> I think that I did not make myself clear enough.
>
> My problem is I do not even know from a pdb file which atoms belongs to
> antigen and which belongs to antibody.

I would suggest using any of the viewers mentioned and just try pointing at a few things.
If you go get my source code, I put references in. Maybe these will help,
( in any case, I think pdb.org is the definitive site for this particular file type )

$ grep http atom/pdb* | grep -v "\.bak:" | unix2dos> /dev/clipboard

atom/pdb_atom.cpp://	http://www.wwpdb.org/documentation/format3.0-dif.pdf
atom/pdb_atom.cpp://	http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html
atom/pdb_atom.cpp://	http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
atom/pdb_chain_maker.h://http://peds.oxfordjournals.org/cgi/reprint/10/7/777.pdf
atom/pdb_chain_maker.h://http://www.umass.edu/microbio/rasmol/rasbonds.htm
atom/pdb_chain_maker.h://http://bioinformatics.oxfordjournals.org/cgi/reprint/17/10/949.pdf
atom/pdb_chain_maker.h://http://deposit.pdb.org/cc_dict_tut.html



>
> For example, for 1JPS.pdb. There are three chains: chain L, chain H and
> chain T.
>
> Part of the pdb is :
>
> ----------------------
> HEADER IMMUNE SYSTEM 03-AUG-01
> 1JPS
> TITLE CRYSTAL STRUCTURE OF TISSUE FACTOR IN COMPLEX
> WITH
> TITLE 2 HUMANIZED FAB
> D3H44
> COMPND MOL_ID:
> 1;
_________________________________________________________________
Keep your kids safer online with Windows Live Family Safety.
http://www.windowslive.com/family_safety/overview.html?ocid=TXT_TAGLM_WL_family_safety_072008



More information about the BBB mailing list