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When I first import a PDB structure, what do the different colors mean?

Maestro color-codes the entry to highlight parts of the protein that need attention. Details are given in the Maestro User Manual.

ORANGE - Non-standard residues connected by geometry and/or CONECT records. Unless duplicate CONECT records are specified, only single bonds are assigned, so you will need to add multiple bonds.

RED - Standard residue, but the input PDB file had missing atoms.

BLUE - A standard residue that has some atom names unknown to the standard connection template. The unrecognized atom names were connected by geometry.

CYAN - An adjacent residue is listed in the SEQRES records but is entirely missing from the ATOM records, indicating a gap in the structure.

GREEN - A residue with an alternate location indicator. The first one listed in the PDB file is the one used to generate the converted structure.

GREY - Standard residues connected by standard templates. Confidence in bond orders assigned to these residues is high.

Keywords: Maestro, PDB, color code

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