Re: [modeller_usage] Regarding Proper Alignment

On 7/28/11 11:49 PM, Ashish Runthala wrote: > May somebody tell me the logic of using > rms_cutoff=3.5 while comparing and aligning multiple structures. Even > when you alter, no difference come up in the generated model.

Changing rms_cutoff will not change the alignment. The cutoff is simply the distance below which two residues are considered to be structurally equivalent when aligned, so it will only affect measures such as the structural overlap (and quality score).

Ben Webb, Modeller Caretaker