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. 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; COMPND 2 MOLECULE: IMMUNOGLOBULIN FAB D3H44, LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: FAB FRAGMENT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: IMMUNOGLOBULIN FAB D3H44, HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 FRAGMENT: FAB FRAGMENT; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TISSUE FACTOR; COMPND 13 CHAIN: T; COMPND 14 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 15 ENGINEERED: YES ----------------------------------- Is chain T antigen, because chain L and chain H are denoted as LIGHT CHAIN and HEAVY CHAIN? Is this a general rule to tell which chain corresponds to antigen? Thank you very much! Li On Tue, Jul 15, 2008 at 11:34 AM, Kalidas Yeturu <[EMAIL PROTECTED]> wrote: > Hi Mr.Li > You may use my program 'get_list_of_all_pair_distances.c' to obtain all > pair distances between atoms in a given PDB file. The program will output > <line-1> <line-2> <distance> > where lines correspond to corresonponding lines in PDB file that have > ATOM/HETATM cards; and <distance>es are in ascending order. > > You can select that pair of lines which correspond to the pair of atoms > from chains you want to find distance. I checked '1jps.pdb' and noticed > that > there are 3 chains L, H and T. > > You may need to tailor the above program to tune the output to your > specific > need. > > With Regards > Kalidas. Y > > On Tue, Jul 15, 2008 at 4:27 AM, Xue Li <[EMAIL PROTECTED]> wrote: > > > hello all, > > > > I am new in this. > > > > If I have 1JPS.pdb, would someone please tell me how to calculate the > atom > > distance between antigen and antibody? > > > > Thank you. > > > > Li > > _______________________________________________ > > BBB mailing list > > [email protected] > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > Kalidas Y > http://ssl.serc.iisc.ernet.in/~kalidas<http://ssl.serc.iisc.ernet.in/%7Ekalidas> > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- Xue, Li Bioinformatics and Computational Biology program Material Science Iowa State University Ames, IA 50010 515-450-7183 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
