Dear all,
I am trying to construct a model with two chains, the conformation of the template is extended helix, However, the conformations of the model I got were folded, the C-terminal is very close to the N-terminal. It is not extended which is what I want.
How can I do to make sure that the conformation of the models are extended?
All the best, Qinghua
On 10/14/13 7:55 AM, fantasticqhl wrote: > I am trying to construct a model with two chains, the conformation of > the template is extended helix, > However, the conformations of the model I got were folded, the > C-terminal is very close to the N-terminal.
This suggests that your alignment is incorrect.
Ben Webb, Modeller Caretaker
Hi Modeller Caretaker,
Thanks very much for your explain on 'restraints failed' and this one.
I am sure that the alignment is correct because the target and template proteins are the same protein.
There are two chains in the template, it is kind of a dimer of one protein. The conformations of both chains are extended helix. What I want to do is to model a copper coordination, two ligands from one chain, the other two from the other chain. All the four ligands locate at the N-terminal.
I don't understand why the conformations of generared modelsl have folded conformations, the C-terminal is quite close to the N-terminal. Could you please give me some suggestions? Thanks in advance!
All the best, Qinghua
On 10/15/2013 12:27 AM, Modeller Caretaker wrote: > On 10/14/13 7:55 AM, fantasticqhl wrote: >> I am trying to construct a model with two chains, the conformation of >> the template is extended helix, >> However, the conformations of the model I got were folded, the >> C-terminal is very close to the N-terminal. > > This suggests that your alignment is incorrect. > > Ben Webb, Modeller Caretaker
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
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
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