Re: [modeller_usage] Is there a way to it?

[Modeller Caretaker <>]

On 01/10/2012 02:05 AM, Ashish Runthala wrote:
> Is there a key to increase gap penalty scheme for different factors,
> like residue compatibility, Solvent Accessible Surface Area, depth of
> residue center from the molecular surface etc.

Sure, if you're using SALIGN, you can simply adjust the weights 
(feature_weights argument). "Residue compatibility" is feature 1; 
surface area is roughly feature 3. For features that SALIGN doesn't 
consider (presumably that's what you mean by "etc" above) you would have 
to calculate them yourself and give SALIGN a user-defined weight matrix 
(feature 6) to use.

	Ben Webb, Modeller Caretaker
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