Good point. Thanks Flavio.
Daron
On May 31, 2013, at 3:54 AM, flavio seixas oivalf_nix@yahoo.com wrote:
> 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 >>