Structure Analysis

There are various tools available for the analysis of structures.

htab

[minimal angle=150°] [maximum bond length 2.9 Å]
[-t]
[-g]

Searches and adds found hydrogen bonds (like HTAB and RTAB in Shelx) into the 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 instructions will be added.

  • -t: adds extra elements (comma separated like in -t=Br,I) to the donor list. Defaults are [N,O,F,Cl,S]
  • -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 p-p 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 constructued of symmetry generated atoms it grow 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=0.2Å]

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, each map voxel is tested, the default quick algorithm, uses the atom masks to find volume occupied by the molecule. The precise calculation is vectorised
  • -r: resolution, a resolution of at least 0.1Å  and -p options 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 the ways is to provide a file name with radii ([element radius] a line format), the other one 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 the 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 it by the same factor.

calcfourier

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

Calculates Fourier for current model

  • -r: the resulting map resolution in angstrems
  • -i: integrate the calculated map
  • -scale: when Olex2 calculates structure factors, it uses the linear scale as a sum(Fo^2)/sum(Fc^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).

calcpatt

 

Calculates and displays Patterson map

match

[atoms]
[-a]
[-w]
[-i]
[-n]
[-u]
[-esd]

This procedure find relation 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 fragments with matching connectivity found, aligns1 them 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 is 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: transfer labels from one fragment to another (two atoms should be provided for from and to fragments. If the value a symbol [or set of] this is appended to the label, '$xx' replaces the symbols after the atom type  symbol with xx, leaving the ending, '-xx' - changes the ending of the label with 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 grown structure is matched
  • -esd: if the variance-covariance matrix can be located (after the refinement with the negative MORE option in the xl), the esd on the RMSD can be calculated using this option

See the 'How to...?' section for more information.

Notes etc about Structure Analysis