On 10/03/2016 04:38 PM, Sushil Mishra wrote:
On Tue, Oct 4, 2016 at 3:43 AM, Modeller Caretaker <modeller-care@salilab.org> wrote:What do you mean by "does not work"? Your script looks fine to me.I mean, in the generated models those restrained atoms (CA of 1 and 169) are far away (>20A) while distance should be somewhere between within 8A.
In that case, most likely either the restraint cannot be satisfied at the same time as satisfying both the S-S bond and your alignment-derived (homology) restraints. You can certainly try building a larger ensemble of models to see if you can sample a conformation that does satisfy all restraints, but more likely you'll have to relax one or more of your restraints (e.g. modify the alignment so that the model can move further from the template).
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage