Thanks alot Ben, i really got it, can you please make me one more thing sure that can i declare any part of my target a coil region irrespective of its alignment wth template region, if yes then how?? cuz in tht example its told about the helix n strand.... but not about coils... thanking in advance Muhammad
Cool Hunk wrote: > i really got it, can you please make me one more thing sure that can i > declare any part of my target a coil region irrespective of its > alignment wth template region, if yes then how?? cuz in tht example its > told about the helix n strand.... but not about coils...
If the model is aligned with a template, you will get spatial restraints that aim to constrain the model to look like the template. So if your template is a helix, and you try to add a strand secondary structure restraint, the two will conflict. So secondary structure restraints only really work in regions of low sequence similarity.
There is no "coil" secondary structure restraint, because "coil" is essentially the lack of any defined secondary structure. It's probably what you'll get by default in unaligned regions. There is no restraint that says "please don't form a helix or strand".
Ben Webb, Modeller Caretaker
There is a way to enforce coil formation: manually modify the reference alignment so that the query is not aligned to the reference in the area of interest. Why do you want to do this?
Jacob Glanville Informatics associate Rinat Biotherapeutics and Bioinnovation Center; Pfizer Inc. (415) 497-3552 Jacob.glanville@pfizer.com
On Aug 5, 2009, at 11:12 AM, Modeller Caretaker <modeller-care@salilab.org > wrote:
> Cool Hunk wrote: >> i really got it, can you please make me one more thing sure that >> can i >> declare any part of my target a coil region irrespective of its >> alignment wth template region, if yes then how?? cuz in tht example >> its >> told about the helix n strand.... but not about coils... > > If the model is aligned with a template, you will get spatial > restraints > that aim to constrain the model to look like the template. So if your > template is a helix, and you try to add a strand secondary structure > restraint, the two will conflict. So secondary structure restraints > only > really work in regions of low sequence similarity. > > There is no "coil" secondary structure restraint, because "coil" is > essentially the lack of any defined secondary structure. It's probably > what you'll get by default in unaligned regions. There is no restraint > that says "please don't form a helix or strand". > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
Jacob Glanville wrote: > There is a way to enforce coil formation: manually modify the reference > alignment so that the query is not aligned to the reference in the area > of interest. Why do you want to do this?
Apologies if I wasn't clear, but that's what I meant in my post - if there is no aligned template, you will basically get coil. But it doesn't *enforce* coil formation by any means - it will essentially try to do protein folding on that region, which could potentially give you any secondary structure type (it is simply that coil is the most likely product).
Ben Webb, Modeller Caretaker
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Cool Hunk -
Jacob Glanville -
Modeller Caretaker