Hello Modeller Caretaker,Thanks very much! I just solved this problem. What I want to model is to construct a model with a copper ion coordinated to two peptides at the N-terminals. I got folded models if I put the copper ion at the C-terminal in the template, while I could get extended models if I put the copper ion at the N-terminal. This may be the wrong alignment mentioned in your previous e-mail. However, I did not have such problems when I tried to construct another model. Maybe the reason is the different templates with different conformations. Anyway, thanks very much!
All the best, Qinghua On 10/15/2013 08:54 PM, Modeller Caretaker wrote:
On 10/15/2013 12:42 AM, fantasticqhl wrote:I am sure that the alignment is correct because the target and template proteins are the same protein.If the alignment is correct (i.e. the restraints generated from the alignment are correct) then the only other possibility is that you have user-defined restraints that are conflicting with the alignment-generated restraints. You can try modeling without them to see if that fixes things. If you can't figure it out, I can certainly look at your input files.Ben Webb, Modeller Caretaker