On 7/20/21 9:01 AM, He, Amy wrote: > 1. About the "Modeller objective function" as an output score for each > model: Could you help me understand what exactly the function is for > the modelling of the missing residues? Is it a score for just the > modelled loop region, or does it include the pair potential between > the loop and the existent structure?

The objective function is simply the sum of all restraints, including the statistical potential, excluded volume, and stereochemistry. It includes the interaction between the loop and the rest of the structure in the final phase of sampling (otherwise the loop would pass through the structure). See https://salilab.org/modeller/10.1/manual/node499.html and the papers cited there for more information.

> 2. About the “md_level” of the loop refinement in > “a.loop.md_level       = refine.<option>”: Comparing the “fast” and > the “large_slow” options, the “fast” option gave me models with > better (lower) values of the “Modeller objective function”. Is this > normal for the modeling of missing residues? Should I rather choose > the “fast” option not the “large_slow”?

The md_level controls the amount of annealing done in the protocol. Generally the defaults are fine here - to get good sampling of conformational space, it is better to build more models with a fast md_level, not fewer models with a slow md_level.

Ben Webb, Modeller Caretaker