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
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
ADDATM identifies atoms in special positions and
places them into
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 P6 22 an atom entered as shown:
atom s1 .1313 .2626 .25
will be printed as:
: x y z mul S1 .1313 2X 1/4 .50
If print priority is set to 4 with a '
reset psta 4 ' line
each parameter constraint will be printed as it is
ADDATM also provides updating and editing
facilities. The "update" mode is switched on by entering
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