Re: [modeller_usage] Minimize structure energy

[Modeller Caretaker <>]

On 1/27/13 3:11 AM,  wrote:
> We wish to perform energy minimization to a model we created. We were
> wondering whether we can use your automodel for that, via "use your own
> initial model":
> http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel

You could use automodel for that if you wanted; just give it a simple 
alignment containing two copies of your sequence (100% identical), e.g.

>P1;orig
structureX:my_model.pdb::::::::
AAAAA*

>P1;seq
sequence:::::::::
AAAAA*

Then set knowns='orig' and sequence='seq' in your Modeller script 
(my_model.pdb is your input model). You don't need to feed in an initial 
model, since the initial model is simply the template already. Note 
though that Modeller builds models that aim to resemble the template 
structure, so it's not going to be able to improve upon the original 
template backbone.

	Ben Webb, Modeller Caretaker
--
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