What should I do about colored residues in my imported PDB structure for Induced Fit Docking?
Colored residues mean that the imported PDB structure has some problems that should be fixed before proceeding. Standard residues that were imported without problems are colored gray. The table below gives some suggestions for the action to take for the colored residues. Most of these problems can be fixed with the Protein Preparation Wizard, which is recommended for preparing proteins for any kind of modeling.
|Red||Missing atoms||Perform a Prime Refinement to predict the missing side chains or loops and use the refined structures. Select these residues for mutation if they are close to the active site.|
|Orange||Missing bond orders||Fix bond orders and formal charges before proceeding|
|Green||Alternate location exists||Select these residues for mutation if they are close to the active site.|
|Blue||Unrecognized atom names||Check for correct assignment|
|Cyan||Missing adjacent residues||Perform a Prime loop prediction to fill in the missing residues and use the predicted structure. Select these residues for mutation if they are close to the active site.|