3.21. DYNAMO: Molecular Dynamics structure factor calculation
| scale | Frel scale factor |
| transf | transformation matrix from archive unit cell to molecular dynamics cell |
| typinf | molecular dynamics data file atom type information |
| format | molecular dynamics data file format |
| maxhkl | maximum and minimum h, k, l and sin / |
| select[a] | select a subset of atoms in the bdf for Fcal |
| omit[a] | omit a subset of atoms in the bdf for Fcal |
| Notes: a. Either select lines may be used, or omit lines, but not both. | |
| DYNAMO | Option | Code | Arg | Def | |
| store Fmd as | frel | ||||
| fcal | |||||
| molecular dynamics | file | name | absolute or relative path to file [a] | ||
| temperature factor | mix | mixed iso and aniso | |||
| iso | isotropic U only | ||||
| ani | anisotropic Uij only | ||||
| ove | overall isotropic, all atoms | ||||
| anom. dispersion | dis | apply dispersion terms | |||
| nod | do not apply dispersion | ||||
| extinction correction | noex | do not apply extinction | |||
| ext | apply extinction correction | ||||
| sin/cos function | nos | calculate from library routine | |||
| sct | use prestored table look-up | ||||
| dataset number | dset | n | use dataset n on bdf | 1 | |
| reflection control | nlis | produce no hkl listing | |||
| lis | s | list hkl with Fobs-Fcal> s | 0 | ||
| nrej | treat all reflections | ||||
| rej | t | reject hkl if rcode >= t | 2 | ||
| Notes: a. file should be the last option on the command line | |||||
| transf | 1-9 | transformation matrix T11, T12, T13, T21, T22, T23, T31, T32, T33 [a] | |
| Notes: a. Transformation is  '=T,
is a column vector of the unit cell vectors
a, b, c. | |||
| typinf[a] | 1- | sequential atom type character code | |
| 2 | number of consecutive sites of atom type in MD file | ||
| 3-4... | as for 1-2, up to 15 types per line, to a max of 40 sequences | ||
| Notes: a. Mandatory sub command line for the DYNAMO calculation. | |||