Dear Tongqing, On Apr 19, 2012, at 5:26 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
> I am trying to use Arp/wArp to build an antibody-antigen complex with 1.65 A > data, there are three chains (heavy, light chains of antibody and the > antigen) in the complex, my question is how to put the sequences in the *.pir > file so that it still identifies different chains. It looks like Arp/wArp > only accepts *.pir file with one sequence id. You can put the chains into a single *.pir file and separate each chain with 10 Alanines. For instance (assuming the antigen is protein): Heavy_chain_sequence_AAAAAAAAAA_Light_chain_sequence_AAAAAAAAAA_Antigen_sequence To do this you need to edit the *.pir file in a text editor. Details on the file format are in the link below: http://www.bioinformatics.nl/tools/crab_pir.html Please contact me if you hit any problems or this suggestion isn't clear. Saul Hazledine
