Re: [modeller_usage] Question about huge gaps

[Daron Standley <>]

Dear Ben,

Thanks Ben,

That's exactly what I needed to know!

Daron

On May 31, 2013, at 3:35 AM, Modeller Caretaker <> wrote:

> 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/
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