3.9. BONDLA: Bond lengths and angles
| atrad | atomic radii by atom type |
| addpek | add peak site to atom list from pek file |
| bond | calculate a specific bond distance |
| angle | calculate a specific bond angle |
| dihed | calculate a specific dihedral angle |
| nviron | calculate distances to a specific atom site |
| site | enter temporary atom sites needed for geometry |
| BONDLA | Option | Code | Arg | Def | |
| bond distances | bond | list all bond distances | |||
| nbon | no bond distances | ||||
| bond angles | angl | list all bond angles | |||
| nang | no angles | ||||
| contact distances | ncon | no contact distances | |||
| cont | list all contact distances | ||||
| dihedral angles | ndih | no dihedral angles | |||
| dihe | list all dihedral angles | ||||
| bond check | chek | for Acta Cryst CIF bond checking | |||
| sort bond & contact distances | nsor | do not sort distances | |||
| sort | sort distances | ||||
| optimally connect input sites | clus | recluster input sites | |||
| nclu | use input sites | ||||
| use full symmetry to searches | symm | apply full symmetry | |||
| nsym | no symmetry | ||||
| do not output geom data to bdf | nbdf | output tobdf | |||
| use brackets in pch output file | brac | no brackets | |||
| number of cells searched | cell | n | 1 for 1 unit cell | 3 | |
| 2 for 27 cells | |||||
| 3 for 125 cells |
| atrad | 1 | atom-type symbol to which the radii apply(max 8 chars) | |
| 2 | maximum radius to be used in identifying contacts | 1.25 | |
| 3 | maximum radius to be used in identifying bonds | 0.9 | |
| 4 | minimum radius to be used in identifying bonds | 0.015 |
| addpek | 1 | atom-type symbol assigned to selected peak sites (max 8 chars) | |
| 2 | number of peaks assigned to atom-type | 1 | |
| 3 | maximum radius to be used in identifying contacts | 1.25 | |
| 4 | maximum radius to be used in identifying bonds | 0.9 | |
| 5 | minimum radius to be used in identifying bonds | 0.015 | |
| 6 | thermal displacement parameter assigned to output site | 0.035 |
| bond | 1-2 | atom labels of sites 1 and 2 (max 24 chars) | |
| 3-4 | numbers [a] of symops applied to sites 1 and 2 | 1 | |
| 5-6 | codes of cell translations applied to sites 1 and 2 | 555 | |
| Notes: a. Symmetry matrix number as entered into STARTX. | |||
| angle | 1-3 | atom labels of sites 1, 2 and 3 (max 24 chars) | |
| 4-6 | numbers [a] of symops applied to sites 1, 2 and 3 | 1 | |
| 7-9 | codes of cell translations applied to sites 1, 2 and 3 | 555 | |
| Notes: a. Symmetry matrix number as entered into STARTX. | |||
| dihed | 1-4 | atom labels of sites 1, 2, 3 and 4 (max 24 chars) | |
| 5-8 | numbers [a] of symops applied to sites 1, 2, 3 and 4 | 1 | |
| 9-12 | codes of cell translations applied to sites 1, 2, 3 and 4 | 555 | |
| Notes: a. Symmetry matrix number as entered into STARTX. | |||
| nviron | 1 | atom label of central site (max 24 chars) | |
| 2 | number [a] of symop applied to sites | 1 | |
| 3 | code of cell translations applied to site | 555 | |
| 4 | radius of sphere to be searched for other sites | 3 | |
| Notes: a. Symmetry matrix number as entered into STARTX. | |||
| site | 1 | atom label of site [a] (max 24 chars) | |
| 2-4 | fractional coordinates x, y, z | ||
| 5 | U | 0.035 | |
| 6 | population | 1 | |
| 7-9 |  x, y, z | 0.0 | |
| Notes: a. If label matches site on the bdf, these coordinates will be substituted for the calculation. Otherwise a new site will be added to the atom list. This site will not be added to the bdf. | |||