Prime User Manual - ISP

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Chapter 12: Command-Line Utilities
12.3 Structure Preparation: primefix.py
Python script for preparing structures for use with Prime, which requires certain conventions
for residue naming. You should not normally need to use this script, because its functions are
performed when you run a Prime refinement job. The script performs the following actions:
• Assigns a unique, single residue name, residue number, and chain name to all ligand residues,
and ensures that new name doesn’t conflict with amino acid residue names.
• Left-justifies 3-character residue names, and ensures that 1- and 2-character residue
names are treated appropriately.
• Converts PDB names to upper case.
• Deletes all bonds to metals and assigns formal charges to the metal and previously
attached atoms. FeS clusters are fixed with the appropriate bonds and formal charges.
• Sets water molecule residue names to "HOH " and PDB atom names to " O ", "1H "
and "2H ". This action is performed for residues named TIP, TIP3, TIP4, SPC, HOH, and
DOD.
• Renames terminal caps: "NME " to "NMA ", pdbname " C " of NMA to " CA ", and
pdbname " CA " of ACE to " CH3".
• Atoms from the same molecule are placed together in the structure output.
Prime can fail if a residue is not in order of connectivity. If this is the case in your structure, it
should be exported from Maestro as a PDB file, then reimported and exported in Maestro
format before running this script.
Syntax:
$SCHRODINGER/run primefix.py infile outfile
infile Input file (Maestro format) containing the structure
outfile Output structure file (Maestro format) containing the prepared structure
Prime 2.1 User Manual