Dear Modellers, I sent this message a few days back too. What is the currently employed path to drive out of the reliable alignment mystery's vicious circle? Tell me a preliminary aspect of the script Salign_Multiple_Struc.py If multiple local folds are present in the computed alignment of this script for different templates, something like this,
Template1>---AAAAAA---BBBBBBBB----* Template2>--APPPAAA---BCBBBB------* Template3>----AAA----BBBBBBBB-----* Template4>----AA-------BB---------*
Elaborate the factors considered by MODELLER to put template2 close to the template1, and why template3 and 4 are kept away from template1 and closer to template2.
Is it minimal RMSD of local template chunks, equal chunk lengths or something else. Give me the complete list of the considered factors considered in MODELLER for such a computation.
Best Regards Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA