Dialog Box: Import File [File menu or button in Startup or Control Window]
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 VIBRATZ data file will be taken from the name of the file, and the title (Title/Axes dialog in the Input1 Menu) will be taken from the data set or phase. The extension .VBR will be appended to the structure file.
File Extension. The three-letter extension (.xxx) which identifies the file type 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 (Input1 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 Settingss 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.
Get atom types from (some formats lack this option). VIBRATZ 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 it is your choice whether this or the atom label (if either) will identify the element.
Import As crystal or molecule. For some file types, such as CCDC, you can import the structure as either molecule(s) or a crystal. The molecule option may give all molecules in the unit cell, not just one.
The following types of file may be imported
----FREE-FORM (.INP) - Files of this type are read and written by ATOMS and CRYSCON (Shape Software). This option can be used to import atomic coordinates from almost any kind of text (ascii) file.
----CCDC FDAT - files from the Cambridge Crystallographic Data Centre.
----SHELX .INS - files from the program system of Prof. G. Sheldrick.
----CIF - Crystallographic Information Files. Some CIF files (with filename extensions .CIF) are "mmCIF" files, containing data for molecules with atomic coordinates on Cartesian axes. See below for possible conversion of these back to fractional crystal coordinates.
----DBWS/LHPM - Rietveld input files.
----ICSD - Inorganic Crystal Structure Database files.
----ORTEP - Original or ORTEP II atom information.
----XTLVIEW - Drawing program.
----ATOMS - Structure drawing program from Shape Software.
----PDB - Protein Data Bank files. These files give Cartesian atomic coordinates for molecules, but may have the information required for transformation back to the original fractional crystal coordinates - see below.
----RIETAN - Rietveld program files.
----GSAS - Data files (.EXP) from the Los Alamos Lab system - may include magnetic vectors.
----AM MINERAL - Data files from the American Mineralogist structure data base.
----FULLPROF - All-purpose refinement program - may include magnetic vectors.
----RAVEL ATOMS - This program is not the same as ATOMS by Shape Software, but is for EXAFS Analysis.
----WIEN2K - The program package WIEN2k performs electronic structure calculations of solids using density functional theory (DFT). VIBRATZ 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) - Files from the International Zeolite Association database (www.iza-structure.org/databases/).
---- GAUSSIAN .FCH or .LOG - Formatted checkpoint or log files from the molecular-orbital program. Cartesian forces from this program can be converted to valence forces.
---- SIESTA - Files from the DFT program (http://icmab.cat/leem/siesta/) Cartesian forces from this program can be converted to valence forces.
Importing PDB files and mmCIF files as Crystals. In PDB files, VIBRATZ 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. In some cases this information is not present - if it is present you will be asked if you want to input the data as a crystal instead of a molecule. 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 used in VIBRATZ are those derived from the transformation matrix, not from the CRYST1 line. After importing, you should check the cell parameters in the Title/Axes dialog and correct the crystal system - because of this problem the cell parameters are always imported as triclinic.
mmCIF files may have the same information, which in these files is in _atom_sites.fract_transf_matrix lines, and the importation procedure is the same.