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Appendix A: Quest Menu Command Summary


Menu LayoutCommands Common to Many Menus


CANCEL            cancel TEST construction.
EXIT              leave QUEST3D.
HELP              invoke HELP system.
REFRESH           restore screen display.
UNDO              revoke last graphics command.

BUILD Menu


2D-CONSTRAIN      access sub-menu.
3D-CONSTRAIN      access sub-menu.
Bond types        active bond type is:
  SING            single.
  DOUB            double.
  TRIP            triple.
  QUAD            quadruple.
  AROM            aromatic.
  POLY            catena forming bond.
  DELOC           delocalised double.
  PI              p-bond.
  ANY             any bond type.
  V.B.T.          variable bond type (follow dialogue).
  V.P.A.          variable point of attachment (follow dialogue).
CHAIN             create chain of length n.
CLEAR             clear current diagram from screen.
COMMAND           by-pass graphics enter TEST manually.
DEFINE-           graphic search TEST complete.
STRUCTURE
DELATMS           delete selected atom(s).
DELBNDS           delete selected bond(s).
DRAW              draw fragment diagram.
Element Types     active element is boxed. Common 
                  elements in BUILD, select OTHER for 
                  PERIODIC-TABLE.
FASTQUEST         initiate search by AND'ing all TESTs.
FUSE              fuse sub-fragments at common bond.
GRID              grid of points to assist drawing (toggle).
GROUPS            access functional GROUPS sub-menu.
LIGAND            build ligand of multiplicity n.
MOVE              move cursor during drawing.
QUEST             access QUEST sub-menu.
REPEAT            build repeat unit of multiplicity n.
RING              create ring of size n.
SPIRO             fuse subfragments at common atom.
TEMPLATES         access TEMPLATES sub-menu.
TYPE              display alphanumeric instruction document.

2D-CONSTRAIN Sub-menu


ALLBOND           all bonds in fragment must be cyclic or acyclic
ALL-EXACT         EXACT constraint applies to all atoms.
CHARGE            charge on an atom.
COMMENT           to introduce a comment line.
CYCLICITY         atom or bond must be part of ring or chain.
DEFINE-           graphic search TEST complete.
STRUCTURE
DICE              Dice coefficient for similarity search.
EXACT             exact number of connected atoms excluding terminal H atoms.
GENERATE-         add terminal H atoms to all C atoms.
HYDS
HYDROGENS         number of terminal H atoms.
MIN-              minimum number of connected 
CONNECTIONS       atoms excluding terminal H atoms.


NO-CYCLIC-        control cyclic substitution (Ex.2).
ROUTES
NO-LINKS          control atomic linkages in fragment (Ex.2).
NOSCREENS         switch off all screens.
NUMBER-OF-        minimum number of occurrences of
FRAGS             search fragment for a hit.


NUMBERS           display atomic numbering of fragment.
SAME-RESIDUE      search sub-fragments must be located in same residue.
SIMIL             similarity search TEST complete.
TANI              Tanimoto coefficient for similarity search.
TOTAL-            total number of connected atoms.
COORD-NO          



3D-CONSTRAIN Sub-menu


DEFINE-           graphic search TEST complete.
STRUCTURE
DEFINE:
  *ALSUN          altona-sundaralingam puckering parameters for 5-membered ring.
  *CREMER         cremer-pople ring puckering parameters.
  *LP2            define angular relationship of vector to sp2 plane.
  *LP3            define angular relationship of vector to sp3 plane.
  *MASK           define non-geometrical attributes.
  ALL-ANGL        define all valence angles.
  ALL-BOND        define all bond lengths.
  ALL-TORS        define all torsion angles.
  ATOM-LABEL      define atom-label.
  PARAMETER       define distance, angle or torsion angle.
DEL-              delete composed instructions.
INSTRUCTIONS
ENANTIOMER:
  INVERT          applies when selecting on torsion angles: fragment can be inverted.
  NOINVERT        applies when selecting on torsion angles: fragment is NOT inverted.
  NORMAL          applies when selecting on torsion angles: fragment inverted if 
                  space group is centrosymmetric.

EXHAUSTIVE        find all occurrences of search fragment.
HIST              specifying of histograms.
INSTRUCTIONS      display of graphical objects (toggle).
MANUAL-MODE       type instructions.
NON-BONDED:
  CONTACT         construction of non-bonded contact between 2 sets of atoms (Ex.5).
  GROUP           define set of atoms for non-bonded search.
  VDW-RAD         modify standard van der Waals radii and/or tolerance limit.

NUMBERS           display of atom numbers (toggle).
OVERLAP           allow overlap of atoms in occurrences of search fragment.
SCAT              specifying of scattergrams.
SELECT            specify limiting values for a parameter.
SETUP:
  CENTROID        setup of centroid.
  DUMMY           setup of dummy point.
  PLANE           setup of plane.
  VECTOR          setup of vector.

SORT              reorder parameter values into ascending order.
SPHERE            specify exclusion sphere.
EXCLUSION


SPHERE            specify inclusion sphere.
INCLUSION
SUMMARY           display of instructions in summary area (toggle).
SYMM-CHECK        controls whether symmetry-equivalent crystal fragments 
                  are eliminated (default) or retained.
TRANSFORM         define new parameters by transformation of old parameters.

SEARCH Menu


BEGIN-AT-         specify refcode at which data
REFCODE           base search begins.
COMMAND           type in single-line instructions.
ELEMENTS          access sub-menu.
FASTQUEST         initiate search by AND'ing all TEST's.
FORMULAE          specify numbers of atoms of elements in single residue or sum formula.
GLIST ANGL        save complete set of valence angles.
GLIST BOND        save complete set of bond lengths.
GLIST TORS        save complete set of torsion angles.
HITALL            declare all database entries to be classed as hits.
H-NORMALIZE       reset lengths of bonds to terminal H atoms.
INFO              general information about set control parameters.
NOJOURNAL         suppress writing to the journal file.
NOSCREENS         switch off all screens.
NUMERIC           access sub-menu.
PDB-SEQUENCE      defining of PDB residue sequences.
PEPTIDE-          access sub-menu.
SEQUENCE
PRINT EXTRA       access PRINT sub-menu.
PRINT NO-HIT      only number of hits are displayed during search.
PRINT REFC        only refcodes and number of hits are displayed during search.
PRINT STAND       reference information in standard format.
QUEST             access QUEST sub-menu.
REDUCED-CELLS     access sub-menu.
RETRIEVE          retrieve sub-database from list of refcodes.
SAVE ASER         save ASER file.
SAVE FBIB         save .bib file (generally not used).
SAVE FCON         save .con file (generally not used).
SAVE FDAT         save .dat file (required for PLUTO).
SAVE MODEL        save .mdl file (can be used in external molecular modelling programs).
SAVE              save .ps file (can be laser printed). 
POSTSCRIPT
SAVE REFC         save .gcd file (list of refcodes).
SCREENS           access sub-menu.
START             initiate screen or similarity search or HITALL has been used.
STATISTICS        generate bit-screens statistics.
STOP-LIMIT        set maximum number of hits in search.
TEXT              access sub-menu.
TYPE              display instruction document.

QUEST Sub-menu


INSIST-ERROR-     bit-screen 33 must be present.
FREE


INSIST-NO-        bit screen 35 must be present.
DISORDER


INSIST- NO-       bit screen 54 must not be present.
POLYMERS


INSIST-ON-        bit screen 153 must be present.
COORDS


INSIST-           bit screen 85 must be present.
PERFECT-MATCH


INSIST-           bit screen 88 must be present.
RFACTOR<=10%
MAXIMUM-HITS      set maximum number of hits in search.
ONLY-ORGANICS     bit screen 57 must be present.
ONLY-             bit screen 57 must not be present.
ORGANOMETALS


QUESTION          combine TEST's using logical operators.
LOGIC             


REBUILD-FRAG      reconstructs defined fragment test in BUILD menu, so it can be modified.
RESET-LOGIC       reset logical combination of tests.
SAVE-DATABASE     save ASER file.
SUBSET
SAVE-FDAT         save .dat file (required for PLUTO).
SAVE-             save .ps file (can be laser printed).
POSTSCRIPT-FILE


SAVE-REFCODE-     save .gcd file (list of refcodes).
LIST


SHOW-             display search information.
CONTROLS
START-SEARCH      initiate search of database.
TERSE             use the symbols + , - for logical operators.
VERBOSE           use the symbols .AND. .OR. .NOT. for logical operators.

Summary of Other Menus

*MASK sub-menu (from 3D-CONSTRAIN)

Set of non-geometrical attributes which can be defined and listed in output summary table, and can be used in statistical analysis. (Vol.2, p.3-15)

EDIT menu

Commands to edit structure constructed in BUILD menu. Allows alteration of: element and bond types; graphical properties of structure, e.g. orientation; content and multiplicity of repeat units. (Vol.2, Chap.5)

ELEMENTS sub-menu (from SEARCH)

Encode TEST's for specified element or set of elements here, (see Section 3.2, Ex.8). (Vol.2, p.10-11)

FILES menu

Used to store and fetch fragments for use in structural TESTs. (Vol.2, Chap.6)

GROUPS sub-menu (from BUILD)

Set of chemical functional groups to speed up drawing of larger fragments. (Vol.2, p.1-47)

NUMERIC sub-menu (from SEARCH)

Encode NUMERIC TESTs here. Full list of fields in Appendix C, (see Section 3.2, Ex.7). (Vol.2, Ch.7)

PEPTIDE-SEQ sub-menu (from SEARCH)

Encode amino-acid sequence TESTs here, (see Section 3.2, Ex.10). (Vol.2, p.10-30)

PERIODIC-TABLE sub-menu (OTHER in BUILD)

Element and element group selection. ELDEF command permits specification of any non-standard element group. (Vol.2, p. 1-25)

PRINT sub-menu (PRINT EXTRA in SEARCH)

Set of extra information items which can be specified to be included in the text area of the display menus, and in the .jnl file. (Vol.2, p.10-41)

REDUCED-CELLS sub-menu (from SEARCH)

Encode TESTs to match a set of unit cell parameters against the reduced unit cell parameters in CSD, (see Section 3.2, Ex.9). (Vol.2, p.10-49)

SCREENS sub-menu (from SEARCH)

Use to assign bit screens for searches, see Section 3.4. (Vol.2, Chap.9)

TEMPLATES sub-menu (from BUILD)

Set of pre-drawn common fragments to speed graphical query construction. (Vol.2, 1-67)

TEXT sub-menu (from SEARCH)

Encode TEXT TEST's here. Full list of fields in Appendix B, (see Section 3.2, Ex.6). (Vol.2, Ch.11)


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