[modeller_usage] Modeller objective function in the modeling of missing residues

To: "" <>

Subject: [modeller_usage] Modeller objective function in the modeling of missing residues

From: "He, Amy" <>

Date: Tue, 20 Jul 2021 16:01:23 +0000

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Dear Modeller experts,

I’m a new user of Modeller and I’m using the x86_64 type of executable on Linux platform. I wanted to model some loop regions which are the missing residues in PDB structure, and basically I follow the “Missing residues” tutorial from the modeler website: https://salilab.org/modeller/wiki/Missing%20residues

I have two questions:

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?

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”?

Thank you for your time and kind advice in advance!

Thanks,

Amy