Hi Eugene,
Thanks for your advice. Can you tell me how to specify restraint strength parameters?
Best,
Li
On Sat, Mar 13, 2021 at 11:16 AM Eugene Radchenko genie@qsar.chem.msu.ru wrote:
> Hello, > > Perhaps you could get around this issue by defining two restraints: one > (perhaps with stronger parameters) for a "definitely helix" region, and > another (perhaps softer) restraint for the "maybe" region or for the longer > overlapping region. In fact, in order to get what you want, you probably > would have to play with the restraint strength parameters anyway – Modeller > can and will "disregard" or partially satisfy some of the restraints if > there are any conflicts. > > Also have in mind that any "ideal helix" you create using restraints could > undergo some distortion or uncoiling when it is left to relax freely (e.g. > during molecular dynamics simulation), so it might not be a big deal if > your defined helix is longer than it actually is. > > Best regards > Eugene > On 13.03.2021 12:31, Li Xue wrote: > > Many thanks for your help. > > Li > > On Thu, Mar 11, 2021 at 10:53 PM Modeller Caretaker < > modeller-care@salilab.org> wrote: > >> On 3/11/21 11:32 AM, Li Xue wrote: >> > Does modeller accept ambiguous restraints? For example, I know there is >> > helix in a region but I am not sure where it starts. >> >> Yes, if you can dream up a function of your coordinates, Modeller can >> restrain it. Built-in restraint forms can be seen at >> https://salilab.org/modeller/10.0/manual/node109.html >> or you can implement your own, as per >> https://salilab.org/modeller/10.0/manual/node480.html >> >> That being said, we don't have an existing restraint that does exactly >> what you describe; you would have to add one. >> >> Ben Webb, Modeller Caretaker >> -- >> modeller-care@salilab.org https://salilab.org/modeller/ >> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >> > > _______________________________________________ > modeller_usage mailing listmodeller_usage@salilab.orghttps://salilab.org/mailman/listinfo/modeller_usage > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >