How to model missing loop by Chimera

Prerequisits

• Chimera (https://www.cgl.ucsf.edu/chimera/)

• Licence number of Modeller (https://salilab.org/modeller/)

Workflow

1. Open a PDB file by chimera.

2. Go to Tools -> Model/Refine loops

3. Select a chain that has a missing loop of interest

4. Press OK, and then two windows appear for the sequence and modelling setting.

5. Select a missing residues, which may be surrounded by a red rectangle if the PDB contains the information of where the missing residues are.

6. Press Apply in the windown Model Loops/Refine Structure.