Prequest: 2.17 Check
On-line Help is available for each button.
The range of Display Functions available include:
Ster: Stereo pairs or single diagram.
Hydr: Toggles display of hydrogens.
Labl: Toggles labelling of atoms: all or none.
Schematic diagram of the 3D Check window
Colr: Colour by elements or monochrome.
Pick: Pick an area of the diagram by polygon enclosure for zooming in on details.
Resi: Select a single residue for display in cases of complex structures with multiple residues.
Cell: Draws the unit cell.
Pack: Draws all molecules having a centre of gravity within the unit cell axial range 0-1.0
+a/2: Extends the range for packing by +a/2
+b/2: Extends the range for packing by +b/2
+c/2: Extends the range for packing by +c/2
Angle: Select any 3 atoms and the angle between them will be displayed on screen.
Tors: Select any four atoms to display the torsion angle on the diagram.
Nodi: Clears the display of all distance, angle, and torsion values.
Intra: Recalculates the intramolecular geometry using the standard CSD covalent radii table and tolerance values, unless these have been re-defined in the BCCAB #RADIUS field.
Inter: Calculates and displays all intermolecular contacts found to be less than the sum of the standard CSD van der Waals radii.
Hbond: Intermolecular contacts are shown when the non-bonded distance is less than the sum of the van der Waals radii for the limited set of atoms C, N, O, F, Cl, Br, I.
Sphere: All intermolecular contacts are displayed within a sphere of given radius. Click on the required atom and then type a radius.
ADDB: Adds a bond between any two atoms by clicking on those two atoms. These extra bonds, not generated automatically by the covalent radius method, are treated as normal bonds and are searchable by Quest.
DELB: Deletes a bond between any two atoms. This is most commonly used to remove extra metal-ligand bonds from metal complexes which cannot be corrected by reducing the atomic radii.
ACOR: Allows direct setting of an atom field in BCCAB. The atom label can be changed and the individual coordinates can be altered.
XCOR: Provides a means of correcting atomic coordinates when there is a discrepancy between the calculated bonds to an atom and the author specified bonds. This situation should be rare for private database creation, but is frequently encountered at the CCDC. PreQuest attempts to suggest a correction coordinate assuming that the other co-ordinates are correct.
CCOR: Provides a means of correcting mis-typed cell parameters. It uses a least squares fit of calculated versus given bond lengths.
BCOR: Provides a correction method for mis-typed author given bonds.
RADJ: Allows interactive adjustment of the covalent radii for a specified element. Click on the atom and then use RAD+, RAD- to adjust the radius by a specified increment.
RAD+: Incrementally increases the elemental radius.
RAD-: Incrementally decreases the elemental radius.
XCAL: Co-ordinate calculation by geometry, based on existing atoms in the structure. Used to complete hexagons or pentagons when an atom is obviously missing.
SHEL1: Display option allowing visualization of a structure by moving outward from a given atom by "shells" of connectivity. Particularly useful for complicated metal complex problems. Used in conjunction with SHEL+: and SHEL-.
METAL: Starts the SHEL1 process on all metals in the structure. Good for metal-cluster problems.
SHEL+: Displays an additional "shell" of connectivity
SHEL-: Displays one less "shell" of connectivity.
SUPP: Suppresses an atom. A suppressed atom no longer belongs to the searchable structure although the information relating to it is kept for future possible use.
Suppression is currently the only method for dealing with crystallographic disorder - minor occupancy sites are currently suppressed at the CCDC during database building.
Select SUPP, then up to 10 atoms to be suppressed, then click SUPP again. The atoms will disappear from the display and be replaced by grey question marks. Repeat this procedure to un-suppress the atoms.
DISOR: Under development - not yet available.
FINDA: Find atom by name and label.
NOSYM: Switch off all symmetry generated atoms displaying only the asymmetric unit of the structure. This is a toggle function.
PreQuest forms a bonded network by applying space group symmetry operations to the atomic coordinates. If the molecular symmetry coincides with some space group symmetry then the program adds the symmetry generated atoms.
CHECK: Runs the 3D Check procedures with messages written at bottom of window (scrollable with the up-arrow, down-arrow keys).
Highlighting of erroneous bonds occurs where appropriate. All calculated bonds are checked for a matching author given bond (#BOND). Bond "errors" are shown according to value of the discrepancy:
MATCH: Attempts to match the chemical connectivity specified in the 2D chemical diagram with the connectivity generated in the 3D structural representation. Each part of the structure is flagged MATCHED or NO MATCH. Missing hydrogen atoms in the 3D structure are allowed by the matching process. Matching problems will not occur if the automatic MAKE2D (section. 2.11) is used.
Note:
It is vital that every molecule in the 3D structure matches a molecule in the
2D diagram because the Quest search for 3D geometric structures will
not access the 3D co-ordinates unless the match status is
"perfect match".
IGVAL: Ignore valency errors. Instructs PreQuest to ignore all of the valency errors that are encountered in checking.
ASSIG: Assigns bond types to the 3D structure. This is a required procedure before Make2D can be applied to the 3D structure. The 3D structure is displayed with bond types depicted as single, double, and triple lines. Dashed lines indicate aromatic or de-localised bonds. Grey dotted lines indicate pi-bonding.
Rules are applied systematically using bond lengths, angles and torsion angles. The method tolerates missing hydrogen atoms. Standard patterns are assigned following CSD database conventions e.g. a perchlorate group has three double bonds, one single bond, and a single negative charge on that single-bonded oxygen.
Full details are beyond the scope of this User Guide, but in general the process is highly successful for organic structures. Some ambiguities can arise with de-localised charge systems, and with some metal complexes.
UNDO: Iteratively undoes each separate stage of edits. The most recent 200 edits for one structure are stored by PreQuest and each can be undone until no more steps are available. Moving to another structure removes the ability to undo edits to a previous structure.
REDO: Iteratively re-applies the edits that have been undone using the UNDO function.
POLYM: This feature is under development for the handling of catena-structures. There is generally an editorial decision to be made as to how much of a polymeric chain should be shown as the motif in the 2D diagram. Various options are given to show:
(18/19 operate as 8/9 but do not restore deleted bonds)
DLONG: Delete all "long bonds" given in the author's bond list (#BOND). These are defined as bond distance > (radius1 + radius2 + tolerance) for the current setting of #RADIUS and #TOLER.
Rset: Resets the display to the minimum overlap view.
Type: Commands can be typed in instead of using the relevant buttons.
Info: Displays brief information on cell parameters, space group, Z value etc.
Help: Short descriptions of the various functions are available.
Quit S: Return to main menu and save the changes made.
Quit D: Return to main menu and discard all of the 3D edits.
Post: Output a postscript file of the current 3D display. Output to file probname.ps
Vy: View down the cell b-axis
Vz: View down the cell c-axis
Vm: View in minimum overlap projection
Zrot+: Rotate clockwise about the z-axis (steps of 3 degrees)
Zrot-: Rotate anti-clockwise about the z-axis
Zoom-: Zoom outwards by scale factor of 10%
Zoom+: Zoom inwards by scale factor of 10%
Size: Scale plot to fit in main window
R: Rotate in steps of 3 degrees
T: Translate in steps of 0.5 Å
Back to Table of Contents
