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