Hi,
Allow me add one more option in this case. You can use a web server that make secondary structure predictions from sequence, e.g. PsiPred (http://bioinf.cs.ucl.ac.uk/psipred/) and use the result to impose any restrictions in the protein modelling, such as alpha helices or beta-sheet.
Regards,
------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br
--- On Thu, 5/30/13, Modeller Caretaker modeller-care@salilab.org wrote:
> From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] Question about huge gaps > To: "Daron Standley" standley@ifrec.osaka-u.ac.jp > Cc: modeller_usage@salilab.org > Date: Thursday, May 30, 2013, 7:35 PM > On 05/30/2013 02:31 AM, Daron > Standley wrote: > > Although I'm not a very regular user of modeller, I > believe it is well > > known that long gaps, especially terminal gaps, look > strange when > > modeled using default options. > > Sure. Typically, we just remove those regions and don't > model them. Any modeling of these regions is just going to > be fantasy anyway. > > > "if distance of residue x from center is greater than > some huge value > > (2-3x the predicted Rg, based on sequence length), add > a bias to the > > potential for x toward the center of the protein" > > The easiest way to do that would be to add an upper bound > distance restraint between each C alpha and the center of > gravity of the protein. An example is at > http://salilab.org/modeller/9.11/manual/node105.html > > Ben Webb, Modeller Caretaker > -- modeller-care@salilab.org > http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >