Hi,
I am not quite sure if I understood your question right, but if you want to apply different level of refinement to different segments of the target sequence, you can do so in a several different ways. One would be to run select segments you want to model thoroughly and run 'loop' routine on them and model the rest of the protein with 'model'. You could even change refinement levels for each of those separately to suit your needs (SET LOOP_MD_LEVEL = 'refine_x' and SET MD_LEVEL = 'refine_x').
I hope this helps...
Thanks, Bozidar
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of margot Sent: Thursday, March 07, 2002 5:14 AM To: modeller_usage@salilab.org Subject: restraints
Hi Modeller Users and Support
if this is a resend, please forgive me - I tried to send this yesterday but it looked like it bounced. The question is: Is there any efficient, systematic way to "soften" or "loosen" homology derived restraints? What I have in mind is to model some (SCR) segments with regular homology derived restraints and others (SVR) with, say Calpha or backbone from the template only, less stringent geometric homology derived restraints and more thorough refinement (i.e. the halfway point between regular homology modelling and loop modelling). Short of editing the restraints by hand - any efficinet way of doing so? thanksalot, margot