MSL Programs:getSurroundingResidues
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A program to select, align and sort by residue type all the residues around a given atom type from a database of pdb files. This is an important utility for answering questions about distributions of atoms/residues around an atom or residue type of interest. For instance, what is the distribution of metal atoms around histidines.
Options
--pdblist List of protein structure files --residue Residue type to search for --searchCenterAtoms Atom types to use to compute distances --distance Distance from searchCenterAtoms to surrounding atoms --alignByAtoms Optional. Atoms to align all the surrounding atoms by on the reference residue type (Default "N CA C") --nmrpdb Optional. Make single NMR-style PDB file for each Residue type pairs (Default Off)
Examples
getSurroundingResidues --pdblist ~/work/pdbs/list.full.txt --residue HIS --searchCenterAtoms "ND1 NE2" --distance 4 --alignByAtoms "ND1 CD2 NE2" --nmrpdb
The above example looks for all histidine residues in a list of pdb files, searching for atoms within 4 angstroms of the ND1 or NE2 atoms within HIS residues. It will then align all atoms by the "ND1 CD2 NE2" atoms of the reference HIS to the first HIS it found. For each residue type around the HIS an NMR-style PDB file will be produced (HIS_ALA.pdb, HIS_ASN.pdb, etc..)
