Atom and Molecule Selection

Base residues

The default behavior is to include all crystallographically-independent molecules (the base residues, a residue being a discrete, chemically bonded unit) in the plot. These are considered as separate items in the molecule list with sequential residue numbers. It should be noted that the centroids of these residues do not necessarily lie in the range (0-1,0-1,0-1) on the crystal axes. The residue membership is based on the concept of discrete, chemically bonded units.

Menu buttons

Calc re-calculates the intramolecular connectivity (i.e. bonds) and re-assigns residues. The criterion for bonding is based on standard bonding radii for each element type, i.e. Dbond <= Ri + Rj + 0.4.

AddB adds an intramolecular bond to the connection list, by clicking on any 2 atoms. The residue membership is recalculated at this time. This may be useful for adjusting the connections around certain transition metals, in complexes where the bonding generated by the radius criterion may not be appropriate.

DelB deletes a bond from the connection list. May also be used to delete non-bonded contacts. The residue membership is re-calculated.

Resi allows the display of one residue in the base set at a time, by clicking on any atom of the residue. To return to the display of all residues, select this button twice.

Typed commands

CALC INTRA (RAD el1 n1 el2 n2) ... (TOL t) (UNIQ) re-calculates the intramolecular connectivity as the menu button Calc but provides more flexibility. The RAD sub-keyword allows the bonding radius values to be changed for particular elements whilst the TOL sub-keyword permits the tolerance to be changed from the default value of 0.4 angstrom. A UNIQ calculation allows atom positions to be moved in order to form discrete residues, and generate symmetry-related atoms where molecules have internal crystallographic symmetry such that the asymmetric unit does not comprise whole molecules. This option is not intended for use with FDAT files derived from the CSD for which symmetry-generated atoms are present already.

HOME moves each original residue to the symmetry-equivalent position in the packing range (0-1,0-1,0-1) where its centroid is closest to the origin. This operation may only be reversed by reading the entry again and is not undone by the Rset button.

Atom selection

Incl includes only a set of element symbols as given, e.g. C N O, or atom names, e.g. C1 O5 Cu1. To return to "include all atoms", click twice on Incl. Include and exclude settings apply to atoms with the same label in all molecules.

Excl excludes a set of element symbols or atom names as given, e.g. C1 N4 H Cl Br I.

HideA may also be used to exclude individual atoms by clicking on an atom in the base set or on a link atom to a molecule in the base set.

Pick allows easy selection of a group of atoms by drawing a polygon around them. This group may be rotated, distances calculated, etc. Is useful for picking out part of a complex structure for close study. May be applied also on packing diagrams enabling slices parallel to planes etc. To cancel select Pick twice, or Rset.

Hydr Hydrogen atom display toggle (command INCL/EXCL HYD), which is independent of the include settings of the H atoms, i.e. Incl/Excl H which also determine whether H atoms are to be included in certain calculations. For an H atom to be displayed it must be Included and the hydrogen atom display toggle must be on.

Typed commands

HIDELA hides link atoms and intramolecular bonds between link atoms.

HIDELB hides non-bonded contact lines to link atoms.

SHOWL restores display of link atoms and non-bonded contact lines.

EXCL INTER removes all link atoms and bonds from the atom and bond lists, irreversibly.

INCL ALL includes all base atoms and associated link atoms, but does not change the status of the H atom display toggle Hydr.

Packing diagrams

Pluto has limits of 1000 atoms, 1500 bonds and 500 molecules which may be drawn in a plot. The unit cell and geometric objects use the same atom and bond storage for their coordinates and connections. If the limits are exceeded, appropriate error messages are produced.

Atoms may not be plotted in positions which are more than +/- 4 unit cell translations from their base molecule positions. If these limits are exceeded, it may be possible to extend the available packing range by moving the original residues into a position closer to each other and to the origin of the crystal axes with the command HOME.

The original base residues are not included in the packing diagram if they lie outside the packing range, although they are still included in the molecule list as shown by Labm.

Menu buttons

Pack displays all molecular residues with centroids in the range (0-1,0-1,0-1) on the crystal axes. Re-selection of PACK will turn this effect off.

+a/2 extends the range by + a/2 in the x axis direction.

+b/2 extends the range by + b/2 in the y axis direction.

+c/2 extends the range by + c/2 in the z axis direction.

Typed commands

PACK x1 x2 y1 y2 z1 z2 generates a packing diagram with all molecular residues with centroids in the range (x1-x2,y1-y2,z1-z2) on the crystal axes.

Packing slices

The menu button Slice allows the selection of a packing slice through the crystal in a given plane. Molecules are considered to be in the packing slice if their centroids are within a specified tolerance distance from the plane along the plane normal and within a specified packing range. It is necessary first to define the packing plane. This will cause a packing slice to be calculated with the current values of the control parameters. The packing slice is calculated on the basis of the last plane to be defined. This plane may be defined by either:

plane defined by selecting 3 atom positions.
plane defined by Miller indices hkl.
plane defined a line drawn on the plot and the vector normal to plot, i.e. a cleavage plane.

The slice button also allows the following parameters to be defined:

select molecules in a unit cell packing range (default 0 1 0 1 0 1).
slice thickness (default 2A). Molecules are included if centroid within this slice, i.e. are less than half this distance along the plane normal from the plane.
define the distance of the plane from origin explicitly.
move the plane perpendicular to the normal by incrementing distance to origin.
colour the plane, default is colour 14 (dark grey)

If no molecules appear with the default settings a larger packing range may be selected (e.g. -1 1 -1 1 -1 1), the slice thickness increased or the plane moved relative to the origin. The plane grid moves appropriately if distance of plane used for packing slice to unit cell origin is changed.

Network expansion

The menu buttons Exp, Strt, Stop and Exp- are used to control the expansion of a non-bonded network from growth points, the link atoms, which comprise atoms in non-bonded contact with the current molecules as derived by the Inter, Hbond or Sphr functions. Link atoms asscociated with the base molecules which are excluded with the HideA button are omitted from the expansion process. They may be restored with INCL ALL.

Network expansion may be started from current molecule list with the Exp button (or the typed command EXP -3) or (re)started from base set with the Strt button (command EXP -1). This causes the Exp button to be highlighted and the link atoms to be displayed with sequential (cyan) link numbers. Only active link atoms (those at which new molecules may be added) are numbered. Selecting Exp button again, followed by clicking on active link atom, causes the molecule containing the link atom to be added to the plot, with any link atoms it may have. The link numbers have no significance except as identifiers allowing expansion by the alternative typed command EXP n.

If the Exp button is clicked again or the sub-keyword ALL (n) is typed instead of selecting or typing a link atom number, the network is expanded on all currently active links. This allows the network to be built up in 'shells' around a central molecule or group of molecules. If the optional integer n follows, expansion proceeds only on links to molecules generated from a particular base residue.

Expansion must start from a molecule or set of molecules with explicit residue numbers (i.e. th residue number is not 0, signifying all residues). Thus, if expanding from the base set, the residue number for the first molecule (the base set) will be set to the residue to which the selected link atom is attached, when expanding on the first link, and the other molecules in the base set will be omitted. By default, expansion on ALL links from the base set expands from residue 1, unless an explicit ALL n instruction is given

Exp may now be used to expand a diagram obtained from Pack, (note that Pack will cancel the effect of any earlier expansion). If Pack and Exp are to be used together, Pack must be selected first. This may be useful if several (non-interconnected) chains of molecules are to be displayed.

Exp- (command EXP UNDO) removes molecules step-wise until the point at which the expansion was last (re)started is reached. If the expansion was started from the base set, the expansion may be undone until the point at which all base residues are plotted is reached.

Stop terminates current expansion sequence (command EXP 0), which also hides the link atoms and turns of link atom numbers.

Editing the molecule list

Menu buttons

HideM provides an interactive means of hiding, grey-shading and restoring molecules in the plot list, allowing molecules to be selected by clicking on atoms.

Typed commands

EDM -n hides molecule m in the current molecule list from the plot. The corresponding entry in the molecule list key shown with Labm is also hidden.

EDM n restores molecule m in the current molecule list to the plot. The corresponding entry in the molecule list key shown with Labm is also restored.

MOLe n tx ty tz RES nres adds a molecule explicitly to the plot list, with symmetry operation n and translations (tx,ty,tz). The RES sub-keyword is used to indicate that the molecule should comprise a single discrete residue nres. Otherwise the atoms in all discrete residues are included (equivalent to RES 0).

The molecule list is scanned for corresponding molecules (same n, tx, ty, tz and nres) and if the same molecule is included already in the list an appropriate warning is given. Note, however, that the same residue may be included twice, both explicitly with RES nres and implicitly with RES 0, so this feature should be used with care.

MOLe NONE removes molecules added explicitly with the MOL command or via the Expand function.

Geometric objects and measurements

Menu buttons

Dist displays distances i-j between any pairs of atoms selected by clicking, or between an atom and a plane, in Angstrom units. Clicking twice displays all distances in the base molecules which are currently included on the plot.

Nodi clears all distances and angles from the plot.

Angl displays angle i-j-k for a set of 3 atoms selected by clicking, in degrees.

Tors displays torsion angle i-j-k-l for a set of 4 atoms selected by clicking, in degrees.

Cell displays single unit unit cell box from (0-1,0-1,0-1) with crystal axes labelled. When toggled off the unit cell is not displayed.

Geom provides a means of adding and deleting planes, vectors and centroids on the plot, as defined by atom positions.

Typed commands.

PLANE n1 n2 n3 ... nN draws a plane on the plot defined by 3 or more atoms with numbers n1 ... nN. The direction cosines for the plane normal and the distance of the plane to the origin are given in the command window, with respect to orthogonal angstrom coordinates referenced to the origin of the crystal axes. Distances of the defining atoms from the plane are also given. Atom numbers are displayed with the LABEL NUM command.

VECTOR n1 n2 draws a vector on the diagram defined by 2 atoms n1 and n2. The direction cosines for the vector and the length of the vector to the origin are given in the command window, with respect to orthogonal angstrom coordinates referenced to the origin of the crystal axes.

DOP n1 n2 n3 n4 allows calculation of the distance in angstroms of a given atom number n4 from a plane defined by 3 atoms n1 n2 n3. The distance is written to the command window.

PLANE NONE deletes all vectors and planes. A maximum of 10 vectors or planes may be defined at one time.