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Structure Analysis

Tools to analyse your structure

[minimal angle=150$^\circ$] [maximum bond length 2.9 Å] [-t] [-g]

Searches and adds found hydrogen bonds (like HTA

and RTA

in Shelx) into a list for the refinement program to add to the CIF. Equivalent symmetry positions are automatically inserted and merged with the existing ones. The command can be executed several times with different parameter values, only one unique instruction will be added.

  • -t: adds extra elements (comma separated like in -t=Se,I) to the donor list. Defaults are [N,O,F,Cl,S,Br]
  • -g: if any of the found bonds are generated by symmetry transformations, the structure is grown using those symmetry transformation

pipi

[centroid-to-centroid distance 4 Å] [centroid-to-centroid shift 3 Å] [-g] [-r=C6,NC5]

The command analyses the \pi-\pi interactions (only stacking interactions for now) for flat regular C6 or NC5 rings and prints information for the ones where the intercentroid distance is smaller than [4] Å and the intercentroid shift is smaller than [3] Å.

  • -g: if any of the rings is fully or partially constructed of symmetry generated atoms, it grows the structure using those symmetry operators.
  • -r: ring content, the defaults are C6 and NC5 rings, the rings are tested for being flat and regular.

calcvoid

[radii file name] [all atoms/selected atoms] [-d=0] [-p] [-r=0.2 Å]

Calculates and displays the structure map. Also calculates the largest channels along crystallographic directions and the packing index.

  • -d: extra distance from the surface (added to the atomic radii)
  • -p: precise calculation where each map voxel is tested. The default quick algorithm uses the atom masks to find the volume occupied by the molecule. The precise calculation is vectorised.
  • -r: resolution, a resolution of at least 0.1 Å and -p option is required to get values for publishing Note: The radii used in the calculation are currently coming from the CSD website:
  • http://www.ccdc.cam.ac.uk/products/csd/radii However there are several ways how the radii can be changed, one of which is to provide a file name with radii ([element radius] a line format). The other is to load the radii from the same kind of the file using >>load radii vdw command.

molinfo

[radii file name] [atoms] [-g=5] [-s=o]

Calculates molecular volume and surface area for all/selected atoms.

  • -g: generation of the triangulation process
  • -s: source of the triangles for the sphere triangulation, [o]ctahedron or [t]etrahedron are available. Generation 5; for octahedron-approximate sphere by 8192 triangles, for tetrahedron by 4096 triangles. Each generation up increases the number of triangles by factor of 4, generation down - decreases by the same factor.

calcfourier

{-calc,- diff, -obs, -tomc} [-r=0.25 Å] [-i] [-scale=simple] [-fcf]

Calculates Fourier for current model.

  • -r: the resulting map resolution in Å
  • -i: integrates the calculated map
  • -scale: when Olex2 calculates structure factors, it uses the linear scale as a $sum(F_o^2)/sum(F_c^2)$ by default, however a linear regression scale can be also used (use -scale=regression)
  • -fcf: Olex2 will use an FCF with LIST 3 structure factors as a source of the structure factors. If this option is not specified, Olex2 will calculate the structure factors using the the reflection used in the refinement (use the >>hklstat command to see more information on reflections).

kill

Atom names or selection or >>labels

Deletes given or selected atoms, bonds or labels. Note that if the bonds are deleted this way they will reappear the next time the structure connectivity is updated. Use >>delbond to remove bonds permanently.

match

[atoms] [-a] [-w] [-i] [-n] [-u] [-esd] [-h] [-cm] [-o]

This procedure finds the relationship between the connectivity graphs of molecular fragments of loaded structure and aligns the fragments. If no arguments are given, the procedure analyses all fragments and in the case when fragments with matching connectivity are found, it aligns Acta A45 (1989), 208 and prints corresponding root mean square distance (RMSD) in angstroms. If two atoms are provided (explicitly by name or through the selection) the graph relation information - orientation matrix and the matching atoms - is printed. Use >>-a option to align the fragments.

  • -a: align the fragments (used when a pair of atoms are provided)
  • -w: specifies weight for the atomic positions - by default the unit weights are used. If this option is given, the atomic position are weighted by the element mass.
  • -i: try to invert one of the fragments.
  • -n: transfers labels from one fragment to another (two atoms should be provided as ‘to’ and ‘from’ fragments). If the value is a symbol (or a set thereof) this is appended to the label. >>$xx replaces the symbol after the atom type symbol with xx, leaving the ending. >>-xx changes the ending of the label TO xx. Note that if the molecules match with >>-i options, this should also be provided for the label transfer.
  • -u: restores the coordinates of the matched fragments - this is useful if the grown structure is matched.
  • -esd: if the variance-covariance matrix can be located (after refinement with the MORE negative option in the xl), the esd on the RMSD can be calculated using this option.
  • -h: calculates the final matching and RMSD calculation without taking H-atoms into account.
  • -o: when overlaying molecules from different structures whole lattices (if packed/grown) are overlayed, not only the two fragments. To use, select an atom in a fragment of one lattice and an atom in a matching fragment of the other lattice. When a selection of two atoms is given the command prints the alignment matrix. This matrix alongside the >>sgen command can be used to generate new atoms. Use the >>-cm option to copy the matrix to the clipboard.
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