The following common variables may be examined (the variable name should be preceded by “#” to indicate that it is a THINK common variable, rather than a user-defined symbol):
| Variable name | Description |
| NTYPES | Number of atom types |
| NMOLES | Number of molecules |
| NATOMS | Number of atoms |
| NFIELD | Number of data fields |
| NTPDUM | Number of dummy atom types |
| NLEARN | Number of records in learn file |
| NFDUSR | Start of user data fields (ie read from files) |
| NTWIST | Number of rotatable bonds |
| NPLTMP | Number of temporary pool addresses in use (internal use) |
| NPHARM | Number of unique pharmacophores in molecule |
| NPDEFN | Number of pharmacophore definitions |
| NRESDS | Number of residues |
| NCYCMX | Maximum number of minimisation cycles allowed during ligand refinement in site searches |
| NITEMX | Maximum number of iterations allowed during ligand refinement in site searches |
| Variable name | Description | See section | Default |
| RCWIDT | Current atom label character width | ||
| RCHEIT | Current atom label character height | ||
| RRWIDT | Requested atom label character width | 8.0 | |
| RRHEIT | Requested atom label character height | 12.0 | |
| XLPORG | X-offset to learn plot origin | ||
| YLPORG | Y-offset to learn plot origin | ||
| XLPWID | Learn plot column width | ||
| NPTSNG | Number of conformational points about single bonds | 3 | |
| NPTCON | Number of conformational points about conjugated bonds | 3 | |
| NPTALP | Number of conformational points about alpha bonds | 6 | |
| NPTAMD | Number of conformational points about amide bonds | 0 | |
| NPTRNG | Number of conformational points about ring bonds | 0 | |
| ICSAMP | Conformational analysis sample size | 1000 | |
| IFDACT | Field containing activity data | ||
| SIGACT | Significance value for activity data | 0.3 | |
| IFDXAX | X-axis field for general plot | ||
| IFDYAX | Y-axis field for general plot | ||
| IFDZAX | Z-axis field for general plot | ||
| RATCPK | Ratio of CPK radius to VdW radius | 0.6 | |
| SCUFTR | Display scale factor (pixels per Angstrom) | ||
| NTWUMX | Limit to the number of rotatable bonds for conformer generation (0=no limit) | 0 | |
| RCNFMX | Maximum number of conformers for conformer generation (0=no limit) | 4.1 | 0 |
| D3DTOL | 3D search distance tolerance | 0.5 | |
| D3DVOL | Ratio of pharmacophore volume to number of heavy atoms | 0.25 | |
| D3DARE | Ratio of pharmacophore area to number of heavy atoms | 0.25 | |
| I3DHMX | Limit to number of substructure solutions considered for 3D search | 1000 | |
| ISTHMX | Limit to number of substructure solutions considered for site search | 10000 | |
| I3DSUG | Number of derivatives to be generated for 3D and site searches | 0 | |
| GSTMIN | Maximum acceptable protein-ligand score for conformer to undergo refinement | 8.5 | 1000 |
| GSTHIT | Maximum acceptable score for protein-ligand interactions | 8.5 | 0 |
| IRSEED | Random seed | 90527531 | |
| ICFHMX | Maximum number of hits accepted for each conformer (0=no limit) | 8.4 | 0 |
| IMLHMX | Maximum number of hits accepted for each molecule (0=no limit) | 8.4 | 0 |
| DSINTR | 0 | ||
| TIMEMX | Maximum time for conformational generation during 3D and site searches (minutes) | 60.0 | |
| RADCEN | Overlap between site points and protein atoms (Angstroms) | 9.1 | 0 |
| COZCEN | Cosine of minimum permitted angle for accessibility check | 9.1 | 0.5 |
| RADSIT | Radius of extended active site (Angstroms) | 9.4 | 8.0 |
| GSITE0 | DG0 for conformer score | 8.5 | -5.48 |
| GSTRES | K in contribution to free energy based on fit of conformer to pharmacophore | 8.5 | 1000 |
| GSTHBD | DGhbond for conformer score | 8.5 | -3-34 |
| GSTLIP | DGlipo for conformer score | 8.5 | -0.117 |
| GSTBAD | DGbad for conformer score | 8.5 | 0 |
| ITILSZ | |||
| DMNLOS | Distance used to allocate distance weightings 3 and 4 to site points | 9.5.3 | 6.0 |
| PSCOMN | Minimum acceptable pharmacophore score | 9.5.2 | 10 |
| PSACID | Pharmacophore score penalty for acid-HDON matching | 9.5.4 | 0.3 |
| PSBASE | Pharmacophore score penalty for base-HACC matching | 9.5.4 | 0.5 |
| Variable name | Description | See section | Default |
| I3DREP | Bit 0: Skip hydrogens in intramolecular Ligand energy in scoring function | 1 | |
| Bit 1: Skip hydrogen interactions in scoring function | 2 | ||
| Bit 2: Reserved | 0 | ||
| Bit 3: Use softer repulsive term in scoring function | 0 | ||
| Bit 4: Site search Simplex systematic vs random start | 0 | ||
| Bit 5: Site search process only best ICFSMX conformers per molecule | 32 | ||
| Bit 6: Reserved | 0 | ||
| Bit 7: Used by CUSTOM RADIUS=[NO]TOLERANCE | 128 | ||
| IMISNG | Missing value bit pattern | ||
| ICFSMX | Maximum number of best scoring conformers to refine per molecule | 100 | |
| ICOBGD | Background colour for display | 15 | |
| ICOFGD | Foreground colour for display | 16 | |
| ICOACT | Colour for active molecules | 4 | |
| ICOINA | Colour for inactive molecules | 2 | |
| IDGMOL | Update flag for GUI list of molecules | ||
| ICCONT | Conformational analysis contacts check (0=ignore; 1=CPK; 2=VdW) | 1 | |
| ICMODE | Conformational analysis search mode (1=systematic; 2=random; 3=sample) | 1 | |
| IDSMOD | Display mode (internal use) | ||
| ILBMOD | Atom label options (internal use) | ||
| IDVMOD | Diversity display mode (internal use) | ||
| IKYMOD | Key display mode (internal use) | ||
| IMKRNG | Used for conformer generation of ring coordinates (see code) | ||
| IDSCNF | Conformer being displayed | ||
| NDSCNF | Number of conformers being displayed | ||
| KDSMOL | Pool address of list of molecules being displayed (internal use) | ||
| IQUMOL | Query molecule number | ||
| I3DDUM | Bit mask controlling calculation of aromatic ring centroids and lipophiles | 3 | |
| IDSTIL | Current molecule display tile | ||
| NDSTIL | Number of molecule display tiles | ||
| MDXTIL | Number of horizontal tiles in window | ||
| MDYTIL | Number of vertical tiles in window | ||
| IREMOT | Remote property calculation flag | 3.3 | 0 |
| IUDMOD | United Devices mode flag | ||
| NSHITS | Number of hits found in the most recent search | ||
| NSTOTL | Number of molecules searched in the most recent search | ||
| NPHCEN | Number of centres in a pharmacophore | 4 | |
| NPHBIN | Number of pharmacophore distance bins | 10 | |
| IPHCEN | Bit mask of centre types acceptable in pharmacophores | 32748 | |
| IPHMOD | Bit mask controlling pharmacophore calculations | 0 | |
| IHALT | Enables/disables pop-up message box on error | ||
| ISUMOD | De novo compatibility flag (=3 for THINK v1.0) | 0 | |
| ITPACT | Bit mask controlling interpretation of activity values | 0 | |
| ISERVE | Client mode flag (internal use) | ||
| ISTALL | Save best hit only or all hits during site search (0=best; 1=all) | 8.5 | 0 |
| ITRACE | Bit mask controlling production of additional tracing output | D | 0 |
Some of these variables may be altered through the LET command. However, it is recommended that the user checks with Treweren Consultants before attempting to modify any common variable, since alteration of some variables (eg the counters) could have catastrophic consequences.