Amanda,
A "/" in the alignment means a chain break for MODELLER. So two chain breaks (in both the template and target sequences) and the requisite number of gaps in the template sequence should work.
Eswar.
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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 MacFarlane, Amanda J. Sent: Monday, December 22, 2003 10:38 AM To: 'modeller_usage@salilab.org' Subject: [modeller_usage] Gaps in pdb file
Dear Modellers,
I'm relatively new to Modeller, and I have a question which I hope has an easy answer. Whenever the pdb file for a solved structure has a gap in the residue numbers (so, for instance, it jumps from residue 300 to 315), I get an error saying that the number of residues in the alignment file and the pdb file are different. How can I fix this problem?
Thanks!
Amanda MacFarlane
Amanda MacFarlane
Autoimmune Disease Group/Diabetes
Ottawa Health Research Institute
Lab N1 Box 221
501 Smyth Road
Ottawa ON K1S 5B7