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Article ID: 1030 - Last Modified: May 31, 2011

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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