Re: [modeller_usage] Question about huge gaps

[Daron Standley <>]

Good point. Thanks Flavio.

Daron

On May 31, 2013, at 3:54 AM, flavio seixas <> 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 <> wrote:
> 
>> From: Modeller Caretaker <>
>> Subject: Re: [modeller_usage] Question about huge gaps
>> To: "Daron Standley" <>
>> Cc: 
>> 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
>> --  
>>            http://www.salilab.org/modeller/
>> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
>> _______________________________________________
>> modeller_usage mailing list
>> 
>> https://salilab.org/mailman/listinfo/modeller_usage
>>