On 03/24/2011 03:13 AM, Lilit Nersisyan wrote:
I try to refine a long loop in my protein model by adding several secondary structure restraints and I've confronted the following problem: some restraints do not have any effect unless other ones are removed from the restraint list. In other words, after removing some of the restraints others start working properly. I would like to know the reasons and how can this problem be solved.
Can you be a bit more specific? Which restraints need to be removed for others to "start working properly"? Modeller simply sums up all of your restraints, so one restraint shouldn't be treated any differently to any other - however, it may have trouble satisfying two restraints if they both apply to the same residue (e.g. you have two different secondary structure restraints, or the residue is aligned with a template).
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage