3.44. PATSEE: Search for molecular fragment
| FRAG | definition of molecular fragment |
| site | atom sites in molecular fragment |
| zmatrix | geometry description matrix |
| rotate | rotational search parameters |
| transl | translational search parameters |
| triple | triple relationship parameters |
| shift | shift coordinates of following atom sites |
| spin | rotate coordinates of following atom sites about Cartesian axes |
| twist | twist following atom sites about connected atom site |
| FRAG | 1 | Use cartesian coordinates on site lines. | cart | ||
| or | |||||
| 1-3 | cell lengths in Å a, b, c [a] | ||||
| 4-6 | cell angles in degrees  ,  ,
[a] | ||||
| or | |||||
| 1- | labels of atoms to be extracted from lratom: of the input bdf | ||||
| or | |||||
| 1 | five membered ring | pent | |||
| benzene planar conformation | benz | ||||
| benzene boat conformation | boat | ||||
| benzene chair conformation | chair | ||||
| Notes: a. These are applied to the fractional coordinates of the atom sites that follow and must be entered if the cell differs from that on the bdf. | |||||
| site | 1 | atom label | |
| 2-4 | coordinates [a] x, y, z | ||
| 5 | relative site weight in search (max 1, min 0) | 1 | |
| Notes: a. Assumed fractional unless the preceding frag line contains the Cartesian code. | |||
| zmatrix | 1 | n1 sequence number | |
| 2 | atom label | ||
| 3 | n2 sequence number | ||
| 4 | distance to atom n1 | ||
| 5 | n3 sequence number | ||
| 6 | n3-n2-n1 angle | ||
| 5 | n4 sequence number | ||
| 6 | n1-n2-n3 n2-n3-n4 torsion angle |
| rotate | Option | Code | Arg | Def | |
| number of rotations applied | ntry | n | auto | ||
| number of solutions saved | nsol | s | 5 | ||
| intra-mol. vector angle resolution | vres | a | 10° | ||
| intra-mol. vector d min/max | vlim q | p q | 2. 6.A | ||
| intra-mol. vectors for Rfom (ratio) | vfom | f | 0.5 | ||
| intra-mol. vectors for pretest (ratio) | vtes | r | 0.1 | ||
| Rfom acceptance threshold | fomt | t | 0.4 | ||
| number of refinement searches | nref | m | 1000 | ||
| random rotation start value | nran | r | 5431 | ||
| rotation start positions about a b c | seta | a b c | 0° 0° 0° | ||
| rotation range about a b c | setr | a b c | auto | ||
| list all intra-molecular vectors | vlis | no | |||
| signal mirror in fragment | mirr | no |
| transl | Option | Code | Arg | Def | |
| number of translations applied | ntry | n | auto | ||
| number of solutions saved | nsol | s | 5 | ||
| inter-mol. vector d minimum | vmin | d | 3.4 A | ||
| inter-mol. vector shift resolution | vres | q | 0.25 A | ||
| Tfom acceptance threshold | fomt | t | 0.3 | ||
| t3sum acceptance threshold | tprt | f | 0.3 | ||
| translation origin as x/a y/b z/c [a] | sets | x y z | 0 0 0 | ||
| translation range as x/a y/b z/c [a] | setr | x y z | auto | ||
| list triplets used in t3sum | tlis | no | |||
| exclude use of t3sum refinement | nots | include | |||
| random translation start value | nran | r | 5431 | ||
| Notes: a. Six values may be entered; three for the rotation/translation fragment and optionally three for the translation-only fragment. | |||||
| triple | Option | Code | Arg | Def | |
| minimum E value used | emin | e | auto | ||
| minimum A of any triple | amin | a | auto | ||
| max number of E's used | nume | n | 100 | ||
| max number of triples used | numt | m | 100 |
| shift [a] | 1-9 | rotation matrix elements r11,r21, r31, ... , r33 | |
| 10-12 | translation vector t1, t2, t3 | ||
| Notes: a. The shift transformation matrix is applied to all atom sites in the next input fragment. | |||