# Changing the Model View

Changing the visual appearance of the molecule

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## compaq

[-a] [-c] [-q] [-m]

Moves all atoms or fragments of the asymmetric unit as close to each other as possible. If no options are provided, all fragments are assembled around the largest one.

• -a: assembles broken fragments
• -c: similar to the default behaviour but considers atom-to-atom distances. It will move all atoms as close as possible to the largest fragment in the structure.
• -q: moves the electron density peaks closer to the atoms.
• -m: disconnects metals, then does compaq -a and then reattaches the metals.

## direction

The command prints current normal in crystallographic coordinates and tries to match it to a crystallographic direction.

## fixhl

Updates H-atom labels according to the labels of the bearing atoms

## grow

[atoms] [-w] [-s]

Grows all possible/given atoms. For polymeric structures or structures that require to be grown several times, Olex2 will continue grow until the operation results in a symmetry element that has been used previously.

• -w*: permits the application of previously used symmetry operations to other fragments of the asymmetric unit. In other words: if parts of the structure have been grown, this command will also generate symmetry equivalent atoms that are not connected to the already grown fragment, i.e. solvent molecules.

If the main molecule is grown, but only one solvent molecule is shown, using >>grow -w will produce other solvent molecules using symmetry operators used to grow the main molecule.

## label

[atoms]

Adds labels to all/given/selected atoms and bonds. These labels can be moved by pressing the SHIFT key while holding down the LEFT MOUSE button, and edited by double-clicking on them.

• -type: {subscript, brackets, default
• -symm: {[], # , full} - if an atom is generated by non-identity symmetry operation, it will be added as a superscript. Note that if # is used as the symmetry identifier then the labels of every type of new atom generated (in growing or packing) should be recalculated. Olex2 will then print current mapping of the symmetry numbers to the symmetry operators. ## 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.

## matr

[1,2,3 or abc] or [abc a1b1c1] or [x11 x12 x13 y11 y12 y13 z11 z12 z13]

Orientates the model along; a (1 or 1 0 0), b (2 or 0 1 0), c (3 or 0 0 1) or any other crystallographic direction e.g. 123, which sets the current normal along the $(1 \times a+2 \times b+3 \times c)$ vector. Two crystallographic directions (from and to) may be specified to align the current view normal along the (to-from) vector. Also a full Cartesian matrix can be specified. If the directions are signed or consist of multiple digits, all components should be of the same length like in 1 2 0 1 0 1 or -1 +1 +1 (same as -1 0 1 0 1). If no Arguments are given, the current Cartesian orientation matrix is printed.

• -r: uses the reciprocal lattice instead of the direct.

>>matr 1 or >>matr a or >>matr 100 - sets the current normal along the crystallographic a direction. >>matr 100 011 sets the current normal along the (0 1 1 -- 1 0 0) direction (the normal direction changes if from and to are swapped)