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Article ID: 417 - Last Modified:

Do you have a utility to clean up a PDB file? I have some PDB files with just simple atom names C, N, O, H instead of unique atom names and Maestro seems to be modifying their names.

This behavior is not unusual as Maestro expects PDB files to be formatted according to the official v2.x or v3.x PDB format, which requires every atom to be uniquely identified. This happens when the file is not a PDB file according to the standard, but a text file with a .pdb extension that looks like a PDB file.

You can make the PDB atom names unique in Maestro. Import the structure into the Workspace, then use the Atom Properties tab of the Build panel. Choose PDB Atom name from the Properties option menu. Click on the "All" button in the second box to "Set unique PDB atom names within residues". You can check if the atoms were renamed correctly with Label atoms → PDB Atom names (on the toolbar).

You might have to convert your irregular PDB file into .mol2 first, and then import the .mol2 file into Maestro. You can use OpenBabel to do the conversion:

In general, PDB files are not optimal for storing structures other than proteins, and irregular PDB files are even more so. For example, sdf or mol2 format is superior in many ways, including explicit bond and partial charge information in addition to the coordinates.

Keywords: Unique PDB atom names, openbabel, PDB format, Maestro

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