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

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