VMD User's Guide

Keyword Arg Descriptionall bool everythingnone bool nothingname str atom nametype str atom typeindex num the atom number, starting at 0serial num the atom number, starting at 1atomicnumber num atomic number (0 if undefined)element str atomic element symbol string (’X’ if undefined)altloc str alternate location/conformation identifierchain str the one-character chain identifierresidue num a set of connected atoms with the same residue numberprotein bool a residue with atoms named C, N, CA, and Onucleic bool a residue with atoms named P, O1P, O2P and eitherO3’, C3’, C4’, C5’, O5’ or O3*, C3*, C4*, C5*, O5*.This definition assumes that the base is phosphorylated,an assumption which will be corrected in the future.backbone bool the C, N, CA, andO atoms of a proteinand the equivalent atoms in a nucleic acid.sidechain bool non-backbone atoms and bondswater, bool all atoms with the resname H2O, HH0, OHH, HOH,watersOH2, SOL, WAT, TIP, TIP2, TIP3 or TIP4fragment num a set of connected residuespfrag num a set of connected protein residuesnfrag num a set of connected nucleic residuessequence str a sequence given by one letter namesnumbonds num number of bondsresname str residue nameresid num residue idsegname str segment namex, y, z float x, y, or z coordinatesradius float atomic radiusmass float atomic masscharge float atomic chargebeta float temperature factoroccupancy float occupancyuser float time-varying user-specified valueat bool residues named ADA A THY Tacidic bool residues named ASP GLUacyclic bool “protein and not cyclic”aliphatic bool residues named ALA GLY ILE LEU VALalpha bool atom’s residue is an alpha helixamino bool a residue with atoms named C, N, CA, andOaromatic bool residues named HIS PHE TRP TYRbasic bool residues named ARG HIS LYSbonded bool atoms for which numbonds > 0buried bool residues named ALA LEU VAL ILE PHE CYS MET TRPcg bool residues named CYT C GUA Gcharged bool “basic or acidic” 77cyclic bool residues named HIS PHE PRO TRP TYRTable 5.5: Atom selection keywords.