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

[Kalidas Yeturu]

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 <me.lixue at gmail.com> 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
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-- 
Kalidas Y
http://ssl.serc.iisc.ernet.in/~kalidas