RE: [modeller_usage] Gaps in pdb file

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: [mailto:] On Behalf Of MacFarlane, Amanda J.
Sent: Monday, December 22, 2003 10:38 AM
To: ''
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

Autoimmune Disease Group/Diabetes

Ottawa Health Research Institute

Lab N1 Box 221

501 Smyth Road

Ottawa ON K1S 5B7