Bond angles may be excluded from the listings with the NOANG sub-keyword. A Berry pseudo rotation analysis is carried out automatically when an atom is found to be bonded to exactly 5 atoms. Note: Symmetry may also be presented in the SHELX-76 style. The EXPAND option may be useful for the generation of a file with the complete molecule as opposed to just the unique part. Labels not conforming with the PLATON-rules are modified in a new label including the symbol #. The atom-name may contain parentheses enclosing the numerical part. UIJ atom_name U11 U22 U33 U23 U13 U12 Anisotropic thermal parameters.
See appendix — I. ATOM atom_name x y z (pop) (sig(x) sig(y) sig(z)) (spop) This specifies the positional parameters, the population and their estimated standard deviations. That is, only expressions of form: «[expr:n]» or «[expr:?n]» are allowed, where «expr» is any legal atomic expression excluding atom maps and «n» is a map class value. Note: Rhombohedral lattice types (in hexagonal setting) should be specified explicitly using an extra symmetry generator. Alternatively, if you are connected to the internet when you run LigPlot+, the required file can be retrieved by ftp from a given ftp site. Each subsequent plot is fitted to the first by a sequence-based comparison of the two binding sites. The right-hand plot shows superposed on it a plot of a similar molecule (9DG) bound to PDB entry 1q2r. The red circles and ellipses identify the residue on the latter plot that are equivalent to the underlying residues from the first plot.
The plots generated by these programs can be interactively edited on screen and then written to a PostScript file for printing or conversion to various image formats. The program will search for the PDB file using the location templates defined in your Paths and Directories parameters described above. Atoms with distances less than the sum of their covalent radii plus a tolerance TOLA (Default = 0.4 Angstrom) are considered to be bonded. The first set allows you to specify which atom-atom contacts are to be included as non-bonded contacts: a) between hydrophobic atoms only (ie C or S), b) between a hydrophobic atom and any other, or c) between any type of atom. Save. Once you have entered all the parameters, press the Save button to store your paths.
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