Dear Modellers, 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. Is this upper bound a relaxed in every modeling case. It may not be so, when same family proteins are aligned. So this strict upper bound on Cα distance may leave several large chunks unaligned. Variable gap penalty makes the alignment correct through flexible allowed superposition, but why changing rms_cutoff didn't generate better models, not even 0.1 GDT_TS improvement was not observed.
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
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