Yes, you can. The only difference is chain breaks are listed in the alignment with a "/" (not a "|").
--- Eswar Narayanan, Ph.D Mission Bay Genentech Hall 600 16th Street, Suite N474Q University of California, San Francisco San Francisco, CA 94143-2240 (CA 94158 for courier) Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 http://www.salilab.org/~eashwar
-----Original Message----- From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Rao, Guru Sent: Thursday, November 13, 2003 6:03 AM To: modeller_usage@salilab.org Subject: [modeller_usage] modeling a dimer
Hi:
I am working with a protein which we have characterized to be a dimer. Homologous proteins are also dimers and the 3D structures are of the dimeric forms. In these proteins, the amino acid sequence of the dimer is represented as A and B chains. Can I model my protein as a dimer by arranging my sequence as A and B chains with a " | " in between? Would appreciate some thoughts. Thanks,
Guru Rao
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