Dialog Box: Import File [ File Menu ]
If there is a data set in memory which has been modified, you are asked if you want to save the changes.
If there is more than one data set or phase in the file, the Data Sets...in Import File dialog will present you with a list. The name of the CRYSCON data file will be taken from the name of the file, and the title (Control Window or Title/Axes dialog in the Input Menu) will be taken from the data set or phase. The extension .CCO will be appended to the structure file.
File Extension. The three-letter extension (.XXX) which identifies the file type under Windows may be specified here - only files of that type will be shown in the Open File dialog. To show all files, enter ".* ".
Source of symmetry (some formats lack this option). If you select Use positions as xyz, in which symmetry operators are given in the form of positions in the general equipoint as in the International Tables , the symmetry option (Input Menu) will be Custom Symmetry. After import, you may need to check the Symmetry option to be sure the centric/acentric choice and the Bravais lattice type are correct (some formats include a center of inversion and/or lattice centerings in the operators and some do not). If you select Space group symbol, the Space Group symmetry option will be used. The Hall symbol, the Hermann-Maughin symbol, and then the International Tables number will be used in that order if present. If you select Use positions as xyz and the information on operations is not present, the symmetry option will default to Space group symbol. The H-M space-group symbol, Hall symbol, and space-group number are always read if present.
If symmetry is present in the "xyz" or operation form, this is usually the safest option However, this option does not give information on systematic extinctions or true d-spacings, which are required for the Powder and Precession options. It is usually possible to derive the correct space-group symbols from the operations using the Get Symbol option in the Custom Symmetry dialog.
Atom types (some formats lack this option). If a distinct atom type number is not present in the input, CRYSCON will try to assign an atomic number to each input atom either from the first one or two characters of the atom label itself, or from a separate atom type label if that is present. In diffraction refinement file formats, this separate atom type label typically identifies the scattering factor, and it may be a matter of operator preference whether this or the atom label (if either) will identify the element.
Note that in the case of multiple atoms with the same coordinates, that is multiple occupancies for a site, CRYSCON consolidates them into one input atom, but preserves the information on the site occupants (see Input Atoms).
File types supported, with the default extension:
**** Free-Form - .inp. This imports files in the free-form format described elsewhere ( Atom Parameter Files ). Note that this format has been expanded, so that essentially all relevant data for a crystal may be entered.
**** CCDC (Cambridge Crystallographic Data Centre) FDAT - .fdt. The files normally contain a unique set of input atoms, which are the same as those required for input of a crystal in CRYSCON, plus in many cases some extra symmetry-derived atoms necessary to complete the molecule; CRYSCON will use only the unique set of atoms, omitting the extra ones.
**** SHELX-93 - .ins. CRYSCON is programmed only for SHELX-93 files, although it may also be possible to read SHELX-76 files.
Symmetry . The Custom Symmetry option will be used. Typically the true space-group symbol can be recovered from the title. CRYSCON will read the SYMM lines in the SHELX file only if they are in standard International Tables format - the translational part must precede the positional part (i.e. 1/2+x, not x+1/2). If the symmetry was copied from the Tables , there should be no problem. You can edit the symmetry operators after they are read in.
FRAG instruction . Atoms listed between this instruction and the FEND instruction will be ignored.
RESI instruction . Atoms listed after this instruction will be included, but not treated in any special way.
Hydrogen atoms . SHELX has several sophisticated ways of locating hydrogen atoms which are not duplicated by CRYSCON. Frequently, the positions of the hydrogen atoms are not in the .INS file, and must be taken from the output. The output lines giving the hydrogen positions can be copied into the .INS file. If this is done, a type or SFAC number must be inserted after the label and before the coordinates. The hydrogen lines can also be put into a separate file and read in with the SHELX +filename include-file instruction.
Most of the instructions in a SHELX file will be ignored. However, CRYSCON may not know all the current instructions. If it cannot identify an instruction, it tries to read the line as an atom line (this is the way SHELX works). If this fails, you are asked if you want to add the first four letters of the line to the list of instructions to be ignored. These instructions-to-be-ignored are at the end of the SCRPTR setup file, separated by spaces and preceeded by the number of instructions. You can edit this list if necessary.
**** CIF (Crystallographic Information Files) - .exp. CRYSCON uses only a small number of the possible data items in a CIF file and recovers only the most basic information. The dictionary file, CIFDIC.SHT (a shortened version of the complete CIF dictionary), must be in the home directory (the directory containing the CRYSCON.EXE file). CRYSCON will read macromolecular (mmCIF) files, and if the crystal-to-Cartesian transformation matrix in the form of _atom_sites.fract_trans_matrix lines, CRYSCON will set up its own matrix so that the Cartesian coordinates may be converted back to fractional coordinates on the crystal axes. See below under PDB files for further details of Cartesian to crystal transformations.
**** DBWS/LHPM Rietveld - .dbw/.lhp. The DBWS and LHPM formats are very similar.
In the Atom type numbers from: box, the Type label option will select the NTYP field which usually contains the elemental symbol for recovery of the scattering factor.
Three different versions of DBWS file are recognized: 9002, 9411 and 9807. Trying to read a 9002 file may cause an error on the first pass, as CRYSCON tries to read according to the later formats, and in that case you will have another chance to read again according to the 9002 format. Files with only one phase are more likely to be read correctly (but please report any problems reading valid DBWS files).
**** ICSD ( Inorganic Crystal Structure Database) - .ret/.cry. Three types of ICSD file are supported:
1) Files from the current CD-ROM database, accessed by the program RETRIEVE. The RETRIEVE files must be written from the DATA window using the PRINT option, not as export files (if there is sufficient demand, export files may be supported). That is, the file should be a copy of what is shown on the screen in the RETRIEVE program.
2) Files from the Canadian Scientific Numeric Database System (CAN/SND). This service may no longer be available. The files are referred to as CRYSTIN.
3) Files in the original CRYSTIN format (or close to it), available from the Netherlands CAOS information system, from ETH (Switzerland) and perhaps other sources. These files are also referred to as CRYSTIN.
Please contact Shape Software if you have ICSD files which cannot be read by one of these options. The best procedure is to send samples of the files by email or an a floppy diskette.
In CAN/SND files, CRYSCON will use the "NA:" line for the title; in RETRIEVE and original CRYSTIN files, CRYSCON will use the first "MINR" line if present, otherwise it will use the "NAME" line.
**** ORTEP - .ort. This imports the unit-cell parameters, symmetry, atomic positions and thermal data from original or ORTEP II files. It does not read the boundary and plotting instructions.
**** XTLVIEW - .xtl. CRYSCON may need to shift the fractional coordinates to insure that the origin is placed on a center of inversion.
**** FULLPROF - .exp. The "User-supplied" non-magnetic and magnetic options (JBT = +-4 or +-5) are not directly supported - crystallographic and magnetic parameters in files using these options will be read as if one of the standard options were used. Magnetic information is always read as vectors in the crystallographic axes (not as polar or other coordinates), and FULLPROF-specific magnetic symmetry is not currently used.
**** American Mineralogist Structure Database - .amc. The American Mineralogist structure database is currently available on the Internet at www.geo.arizona.edu/xtal-cgi.test. This may change, but the database should be locatable by searching for American Mineralogist.
**** GSAS - .exp. The General Structure Analysis System (Los Alamos) can give magnetic moment vectors.
**** RIETAN - .xyz. This format gives complete symmetry operations, including a center of inversion and lattice centerings if present, as numeric matrices. CRYSCON will convert the matrices to "xyz" form and use the Custom Symmetry option. It will also attempt to identify the center of inversion and lattice centerings and will remove them with your approval.
**** ATOMS (Shape Software) - .str. CRYSCON will read and store data on atom colors and radii from these files. Such data will be written into free-form (.inp) files when exported, and can then be read back into ATOMS.
**** VIBRATZ (Shape Software) - .vbr. CRYSCON will read the main data files (.vbr) from the Windows version.
**** PDB - .pdb. PDB files are intended primarily to present data on protein structures as molecules, and the atomic coordinates are always given in Cartesian form. However, CRYSCON can use the information in the SCALEn lines (Cartesian to crystal transformation matrix) and the CRYST1 line to recover the fractional coordinates and space-group symmetry for the original crystal, through the CRYSCON transformation. In some cases this information is not present - if it is present you will be asked if you want to import the matrix. Note that the transformation matrix given in the SCALEn lines is sometimes not sufficiently precise (because of limitation to 6 places after the decimal point) to recover the original unit-cell parameters (as given in the CRYST1 line) precisely. The cell parameters derived by CRYSCON for the new crystal are those derived from the transformation matrix, not from the CRYST1 line. After importing, you should check the cell parameters and correct as necessary.
The transformation matrix is imported into the Transformation dialog, and the space group for the crystal will be that for the new crystal. The old "crystal" will have the original Cartesian atomic coordinates, and space group P1. In the Transformation dialog, specify the transformation type as Input Atoms Only, so that CRYSCON will not try to fit the original atoms in a unit cell (if you specify Full Unit Cell there may be no generated atoms, as the "unit cell" is only 1 Angstrom on a side.
The Input Atoms Only option will not try to generate the atoms in the New unit cell, or try to check whether all atoms are symmetry-unique. If redundant atoms are present, a further cycle may be necessary. In the Control Window, click the New to Old button, Then Transform. The matrix for this step should be the unit matrix, and the symmetry for Old and New should be the crystal symmetry, that is the symmetry for the original crystal. Use the Full Unit Cells option.
**** RAVEL ATOMS - .inp. This program is not the same as ATOMS by Shape Software, but is for EXAFS Analysis.
**** WIEN2K - .stw. The program package WIEN2k performs electronic structure calculations of solids using density functional theory (DFT). CRYSCON will read the .struct input files, but will only recognize file extensions with three characters, so it may be necessary to rename the files, search manually in the File Open dialog (enter *.struct) or use the "all files" option. Some files may have the space-group number and symbol, but the orientation may be ambiguous and Use positions as xyz should normally be selected in the Import File dialog.
**** IZA (zeolites) - .iza Files from the International Zeolite Association database.