[BiO BB] how to calculate the atom distance between antigen and antibody
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
> 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
> TITLE CRYSTAL STRUCTURE OF TISSUE FACTOR IN COMPLEX
> TITLE 2 HUMANIZED FAB
> COMPND MOL_ID:
Keep your kids safer online with Windows Live Family Safety.
More information about the BBB