Authors: James Stewart, Nick Spadaccini and Syd Hall
Contact: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia
ADDATM places atom and general parameters on the archive bdf. Atoms in special positions are detected and the symmetry constraints on variables are stored in the bdf .
ADDATM provides for the ab initio addition of data to the logical record lratom: on the bdf, and can also edit existing data on the input bdf. ADDATM also detects atoms in special positions and generates the appropriate constraints for positional and thermal parameters.
The parameters loaded by ADDATM are of two types; general structural parameters and atom specific parameters.
Three general structure parameters are loaded by ADDATM as a function of data set. F-relative scale factors for each scale group with a scale line; overall isotropic thermal parameters with uov; and extinction parameters with extinct.
Specific atom parameters are placed in the bdf record, lratom:. The following list of atom parameters are loaded using the control lines atom, link, u, uij and suij:
atomic coordinates,
H atom linkage calculation
atomic thermal displacement parameters,
population parameter,
anomalous population parameter,
and standard deviations for those parameters.
ADDATM identifies atoms in special positions and places them into lratom: with the correct atom multiplicity set. The constraint information required by refinement programs is stored in lrcons: of the bdf. Special positions are detected by transforming the input x, y, and z over all the symmetry operations and testing if any position is within 0.0005 of the unit cell edge of the parent atomic coordinates.
Special position constraints are determined from the application of atom parameters to the 4x4 symmetry matrices (i.e. rotation plus translation operations). This provides the constraints and interdependence of atomic coordinates and thermal parameters due to symmetry. The printed output of the atom parameters indicates that a given atom is in a special position by placing symbols instead of the decimal fractional coordinates entered in the data input stream. The notation is the same as that which is listed in the International Tables for Xray Crystallography, Vol. I. Thus in space group P6122 an atom entered as shown:
will be printed as:
If print priority is set to 4 with a 'reset psta 4' line each parameter constraint will be printed as it is transferred to lrcons: of the bdf.
ADDATM also provides updating and editing facilities. The "update" mode is switched on by entering upd on the ADDATM line. This causes existing atom sites from the input archive bdf to be placed into the atom list. Input atom/linkatomg/u/uij/suij lines will either modify existing atom site data if atom labels match, or be added to the list iflabels do not match an existing site label. Note that all u lines must still be preceded by an atom line with the same atom label.
The stack, rename, delete and editu controls apply in both ab initio and update modes. These lines must be entered after any atom/atomg/u/uij/suij lines have been entered. stack lines are used to sort the sites in the atom list. The first entry will determine the sites at the top of the list. Up to 100 antries are permitted on any number of stack lines. The rename line is used to change atom labels. Atom-type symbols may NOT be entered. delete lines are used to delete sites from the atom list. An atom label is used to delete a single atom and an atom-type symbol is used to remove all atoms of that type. editu lines are used to change the U values of atom sites or atom types. Individual isotropic values may be entered or atoms converted between isotropic and anisotropic.
The invert line to change the enantiomorph-polarity of the structure by inversion in a point. The algorithm is described in Appendix B of Benardinelli and Flack (1985). A suitable point of inversion is found (in some cases the origin cannot be used). In the case of the 22 space groups forming the 11 enantiomorphic pairs, the space group has to be changed into the opposite member of the pair. No user intervention is required in this procedure.
The link line adds geometrical atom site recalculation information to the archive. This is only required for riding atom model refinement using CRILSQ! Existing link information may be purged from the archive by running ADDATM upd plink. Link information is automatically generated by both PIG and CALCAT programs. In the case of PIG this link information may be omitted by invoking the control line PIG nolink whenever H atom are to be built from within PIG.
ADDATM atom S .202 .798 .91667 2.0 .5 uij S .009162 .009162 .001205 .04581 0 0 atom O .498 .498 .66667 2.0 atom C1 .488 .096 .038 2.5 |
The atoms S, O and C1 are loaded onto the bdf with mixed thermal parameters.
Cruickshank, D.W.J. 1956. The Determination of the Anisotropic Thermal Motion of Atoms in Crystals. Acta Cryst. 9, 747.
Henry, Norman F. and Lonsdale, Kathleen. 1965. Eds. International Tables forX-ray Crystallography Vol. 1. Birmingham, England: Kynoch Press.
Bernardinelli, G. and Flack, H.D. 1985. Acta Cryst. A41, 500-511.