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

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