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 =
I hope this helps...
[">mailto:] On Behalf Of margot
Sent: Thursday, March 07, 2002 5:14 AM
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?