Hello all,
Does modeller accept ambiguous restraints? For example, I know there is helix in a region but I am not sure where it starts.
Best,
Li
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
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 >
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 mailto: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 > 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 > 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 mailto:modeller-care@salilab.org > https://salilab.org/modeller/ https://salilab.org/modeller/ > Modeller mail list: > https://salilab.org/mailman/listinfo/modeller_usage > https://salilab.org/mailman/listinfo/modeller_usage > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > 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 >
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 mailto: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 mailto: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 >> 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 >> 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 mailto:modeller-care@salilab.org >> https://salilab.org/modeller/ https://salilab.org/modeller/ >> Modeller mail list: >> https://salilab.org/mailman/listinfo/modeller_usage >> https://salilab.org/mailman/listinfo/modeller_usage >> >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage@salilab.org mailto:modeller_usage@salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage https://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org mailto:modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > 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 >> >