Re: [modeller_usage] extended conformations

[fantasticqhl <>]

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