Re: [modeller_usage] loop refining of a multi chain protein

subarna thakur wrote: > Thanks for suggestion ,it worked. After running the script two PDB files > are generated one with extension .BL00010001 and other with .IL00000001 > extension.Which one should I select and on which basis?

See http://salilab.org/modeller/9v6/manual/node439.html

The generated loop models have the .BL extension. The .IL files are initial loops, which are unoptimized - you don't want to select those.

Ben Webb, Modeller Caretaker