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.

Color	Meaning	Action
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

Keywords: Maestro, PDB, color scheme

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