User:Eric Martz/How JSmol works: Difference between revisions

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==Displaying Molecules==

JSmol is designed to display data files that contain atoms; that is, atomic resolution molecular models. The data file lists atoms, specifying the position in space of each atom (usually in Cartesian coordinates X, Y, Z), the chemical element of the atom, and for macromolecules, the amino acid or nucleotide residue name to which the atom belongs, its position within the residue (e.g. alpha carbon, beta, gamma, etc.), the polymer chain to which the residue belongs, and its sequence number.

JSmol is designed to display data files that contain atoms; that is, atomic resolution molecular models. The data file lists atoms, specifying the position in space of each atom (usually in Cartesian coordinates X, Y, Z), the chemical element of the atom, and for macromolecules, the amino acid or nucleotide residue name to which the atom belongs, its position within the residue (e.g. alpha carbon, beta, gamma, etc.), the polymer chain to which the residue belongs, and its sequence number, etc.

Such molecular structure data files are called [[atomic coordinate files]]. JSmol is able to read more than 50 formats of such files. The most common are XYZ format for small organic compounds (usually <100 atoms), and PDB or mmCIF formats for macromolecules.

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 ==Displaying Molecules==
-JSmol is designed to display data files that contain atoms; that is, atomic resolution molecular models. The data file lists atoms, specifying the position in space of each atom (usually in Cartesian coordinates X, Y, Z), the chemical element of the atom, and for macromolecules, the amino acid or nucleotide residue name to which the atom belongs, its position within the residue (e.g. alpha carbon, beta, gamma, etc.), the polymer chain to which the residue belongs, and its sequence number.
+JSmol is designed to display data files that contain atoms; that is, atomic resolution molecular models. The data file lists atoms, specifying the position in space of each atom (usually in Cartesian coordinates X, Y, Z), the chemical element of the atom, and for macromolecules, the amino acid or nucleotide residue name to which the atom belongs, its position within the residue (e.g. alpha carbon, beta, gamma, etc.), the polymer chain to which the residue belongs, and its sequence number, etc.
 Such molecular structure data files are called [[atomic coordinate files]]. JSmol is able to read more than 50 formats of such files. The most common are XYZ format for small organic compounds (usually <100 atoms), and PDB or mmCIF formats for macromolecules.