Hello everybody,
I would like to know how you model helices with a gap or insertion (pi or 310 helices). I noticed that if the gap / insertion is in the middle of the helix, Modeller arranges it quite nicely with the alpha restraint. But how can I solve this problem if the gap / insertion is at the very end of the helix?
Thank you for your answers! Julian
On 04/22/2014 04:32 AM, Julian wrote: > I would like to know how you model helices with a gap or insertion (pi > or 310 helices). I noticed that if the gap / insertion is in the middle > of the helix, Modeller arranges it quite nicely with the alpha restraint. > But how can I solve this problem if the gap / insertion is at the very > end of the helix?
Modeller will do the best it can in this case, but the only information it has to use here is the CHARMM forcefield, so most likely you will get an unstructured region.
Ben Webb, Modeller Caretaker
Exactly, I get an unstructured region. I tried to solve this problem by placing alpha restraints at different positions but haven't been successful yet. Maybe anybody has experiences with this?
In any case it would be very nice if pi and 310 helices could also be introduced in future releases.
2014-04-22 23:21 GMT+02:00 Modeller Caretaker modeller-care@salilab.org:
> On 04/22/2014 04:32 AM, Julian wrote: > >> I would like to know how you model helices with a gap or insertion (pi >> or 310 helices). I noticed that if the gap / insertion is in the middle >> of the helix, Modeller arranges it quite nicely with the alpha restraint. >> But how can I solve this problem if the gap / insertion is at the very >> end of the helix? >> > > Modeller will do the best it can in this case, but the only information it > has to use here is the CHARMM forcefield, so most likely you will get an > unstructured region. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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Julian -
Modeller Caretaker