> Date: Wed, 16 Jul 2008 15:20:08 -0500 > From: [EMAIL PROTECTED] > To: [email protected] > 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 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
