On 1/27/13 3:11 AM, danashah@post.tau.ac.il 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