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.

 

---

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