[modeller_usage] Regarding Proper Alignment

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.

Thanks Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA