Dear Derek!
It is not very clear what do you want to do, but it looks like you do not want to use information in the templates. I know two ways to forget about the templates. First is to model the model based on the identical alignment with the model itself (you will be chained to original structure though - not a lot of room to optimize), second is to dealign the alignment with templates completely. Then MODELLER will use it's own homologueless general scoring function to minimize the structure. So far we know that this function works oK for short (<10 res) loops.
Hope this helps.
Derek Smith wrote: > > Dear Modellers > > I have a manually constructed model protein, which I would like to refine > using the MODELLER default schedule. I have attempted this using the protocol > based on question 12 in the MODELLER FAQ. However, I find that MODELLER reads > the model.ini file, and then extracts restraints from the templates, which > are then used in the optimization of the model. I would like to refine my > model based only upon my initial conformation. Is this possible do do, and if > so, how should I go about it?
-- - Dr. Azat Badretdinov - Molecular Simulations Inc. - 9685 Scranton Road - San Diego CA 92121-3752 - Phone: (858) 799 5728