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 >

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 >

Hi Eugene,

Many thanks. I will try the overlapping regions. That sounds like a good plan!

Best,

Li

On Sat, Mar 13, 2021 at 4:11 PM Eugene Radchenko genie@qsar.chem.msu.ru wrote:

> Hello Li, > > Oops, I forgot that Modeller's secondary structure restraints actually > create a whole set of low-level restraints (on angles, distances, etc), and > tweaking their individual strength is not possible. > > Still, having several overlapping restraints (e.g. on residues 1...20 and > 5...15) should make the restraint on 5...15 stronger, although the tail > regions will also be helical if nothing is conflicting with the 1...20 > restraint. > > Hope this helps, > > Eugene > On 13.03.2021 16:04, Li Xue wrote: > > 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 >> >