The Clean command performs a number of operations that prepare the molecule for a molecular dynamics simulation, some of which are accessible via other commands:

• Delete NMR dummy Q atoms (element 0).
• Detect missing bonds and add them.
• Rebuild side-chains with missing atoms
• Delete terminal residues with incomplete backbone, that often occur in X-ray structures when the chain enters a disordered region.
• Delete atoms that are present more than once at alternate locations, keeping those with the highest occupancy.
• Delete molecules that overlap significantly with other molecules and are most likely the result of incorrect PDB format usage, like 1GTV.
• Delete residues that overlap significantly with other residues and are most likely slightly different ligands bound to the same active site, e.g. BTN/BTQ in 2F01.
• Make external single atoms bound to a residue part of this residue, for example the three oxygens bound to Cys 25 in 9PAP.
• Add terminal oxygens
• Reassign bond orders.
• Add missing hydrogens (hints how to handle unwanted hydrogens can also be found there).
• Correct hydrogen names
• Correct incorrectly shifted atom names
• Correct hydrogen naming conventions for methylene, amide and guanidine hydrogens to facilitate stereospecific NOE assignments
• Check and correct flipped CG and CD atom names in Val and Leu residues
• Check and correct OT1/OT2 atom names in amino acids
• Check and correct bond orders and oxygen atom names in (de)protonated carboxyl groups
• Replace seleno-methionine with methionine.
• Add cysteine bridges between close CYS SG atoms that do not already carry a hydrogen.
• Sort backbone and side-chain atoms.

CleanObj 1crn

Prepare object 1crn for simulation.