Re: [modeller_usage] How to get various conformar for a modelled protein?

[Karsten Suhre <>]

Dear B.Nataraj,

>       For my modelled protein, I want to analyis  various possible
> conformare it can assume,In that connection I want to know what is the
> command or  in build routine to create all possible conformation for my
> modelled protein ? Thank you in advance.

  if you are looking for different conformations, you will also need templates 
that exhibit different conformations. Homology modelling can only build 
models that are structurally close. If this is the case, I would use a shell 
script around the call to modeller and vary the name of the template. 
Otherwise, you would have to look for something that comes close to ab-initio 
folding - but that is a domain that is not yet very mature for larger 
proteins..

  I hope this helps, 

  Kind regards, Karsten.