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Data File Descriptions

In general, all computations in the IUMSC are done on IBM compatible microcomputers. Thus, most of the data files are in formats that are readable by IBM compatible systems. Most critical data are in ASCII format. If a structure completed in the IUMSC has been placed in the IUMSC Web data libraries, the hyperlink "Report and Data files for nnnnn" from the crystal data summary page will list the files that are available. The following define the contents of the files that are usually present:


Caution! All data on the IUMSC Web server are protected by US copyright laws. Contact the IUMSC prior to use.

  • anything.gif: An image file that should be viewable using a properly configured .gif viewer
  • nnnnn.tab: The ASCII text file used on the crystal data summary page
  • nnnnn.crt: Cartesian coordinates for the unique molecule
  • nnnnn.sdt: Final Standard Data Tape (SDT) used in IUMSC XTEL library
  • nnnnnA.sdt: SDT which contains symmetry generated information, etc.
  • nnnnn.da: Distances and angles with esd's
  • nnnnn.xyz: Fractional coordinates (suitable for inclusion in publications)
  • nnnnn.us: Anisotropic thermal parameters
  • nnnnn.fo: Fo/Fc listing (print with HPLJ PCL equipped printer)
  • nnnnn.rep: Complete report without Fo/Fc table, summary, and figures
  • nnnnn.sum: Summary, most likely binary file in WP, WordStar, or similar format
  • nnnnn.txt Summary in ASCII format (no subsscripts, superscripts)
  • nnnnnlb.zip The complete library in compressed format (PKZIP'ed)

The compressed (nnnnnlb.zip) library can be downloaded to an IBM compatible system and uncompressed using the PKUNZIP.EXE utility from PKWare. The shareware version of the PKWare software is available in the XTEL library. The following describes the files that are available in each library.

Indiana University Molecular Structure Center Zip Libraries.

For each crystal structure determined at the Indiana University Molecular Structure Center a condensed library file 9nnnnlb.zip is saved. This condensed file is created using software (PKZIP) from PKWARE, 9025 North Deerwood Drive, Brown Deer, WI 53223.

All condensed and binary files are for IBM compatible systems.

The typical structure center library, saved as 9nnnnlb.zip on the IUMSC web server contains many or all of the files listed and defined below. Note that each crystallographer at the IUMSC has personal preferences regarding files that are saved. Note that a few files not listed below may be contained in the libraries. They have been saved for the convenience of the crystallographer and should be fairly self-explanatory to anyone familiar with x-ray crystallography. It is also important to note that over the years some of the files have changed slightly. In most cases all older files are still compatible with present programs.

9nnnn.rep The structure center report, put together by the program MSCREP. This is the report as you know it, without graphics and without the summary file.

9nnnn.sum Summary file for the report. For newer structures it will be written in WordPerfect (several versions are or have been used), for older structures in WordStar.

9nnnn Final standard data tape (T21F) put together, i. e. the tape contains the full contents of the asymmetric unit. It does not contain atoms related by crystallographic symmetry. Atoms related by crystallographic symmetry can be generated using SHORTEP.

9nnnnA The standard data tape with the suffix A, usually contains the complete molecule of interest. It has been put together using the crystallographic symmetry, either by using the BUILD command in SHORTEP or by using the appropriate 401, 405 and 406 commands. This tape is used for the ORTEP plots. Different crystallographers at the IUMSC may use a different nomenclature. JCH, for example, uses T20A for the ORTEP plots in the report.

9nnnnAXH This tape is again the complete molecule of interest, hydrogen atom coordinates have been changed so that the C-H bondlength is lengthened to 1.08A, the isotropic thermal parameter for H is set to 0.5. This tape is usually used for space-filling plots, and also for ORTEP plots.

If the asymmetric unit contains more than one complete molecule, a molecule plus solvent molecule(s), or anion(s) and cation(s), there may be files labelled 9nnnnB, 9nnnnC, etc. Some of these files were created for the convenience of the crystallographer, perhaps for special plots for the report. They can all be regenerated by using the 9nnnn tape and SHORTEP.

agnost.inp Input file for the absorption correction program AGNOST. File contains the orientation matrix for the crystal, as well as the indices of the crystal faces and their distances to a common center in the crystal, in cm, and the linear absorption coefficient mu for the molecule.

agnost.sum Summary file from the AGNOST program. File contains a copy of the input file, max. and min. and average values of the absorption correction (transmission), and the value of mu used for the computation.

ang.dat File of angle data collected for use in the unit cell parameter determination. QACELL. Reflections are carefully centered at plus and minus two theta. File contains h, k, l, two theta, omega, chi, phi and count FORMAT is (3I5,4F8.2,I8).

ang.drx Angle file created by the SEEK program in PCPS. File is used as input to the DIRAX program. DIRAX is an indexing program written by Albert J. M. Duisenberg, Acta Cryst (1992) 25, 92-96.

ang.dxo Output file created by the DIRAX program. It shows the original choice of unit cell made by DIRAX, this may not necessarily be the unit cell used for the solution and refinement of the structure.

angs.inp Input file for ORTEP plots. File contains the orientation angles for the particular views used.

angs.out File containing angles used for the ORTEP-plots in the report. This file is generated from the plotting program COMM. Each time a 10 instruction is issued a set of angles for the particular orientation is saved to the angs.out file. May also occur as angsA.out, etc. to go with ORTEPA.inp etc. File is renamed to angs.inp before running ORTEP.

anyda.out Output from program ANYDA. File contains distances and angles not included in Table 5. File is normally edited and included in the report as Table(n).

app2 File used by KFS. It is an Appendix to Table 2 of the report, containing details of the absorption correction. WES uses Table2a for this information.

avoid.out File created by the program AVOID. This program is used when checking a completed structure for areas (voids) where a poorly defined solvent molecule might be. This file may also be saved as Table of Molecular Packing Analysis.

bmfit.sum File containing a summary of a best molecular fit of two molecules. File is created by the program BMFIT. This file may also be saved as Table(n), see below. The BMFIT program is used when comparing the structures of similar molecules.

center.lst File of centered reflections collected by the SEEK program. This file is used in the initial stages of defining the unit cell and lattice for a crystal.

crystal.acd File created by the program CRYSTAL and also by AGNOS, file is used to view the crystal shape with the program ACROSPIN.

crystal.prn A copy of an ORTEP.PRN file. The file shows the crystal shape used for the AGNOST input. Files used to create this plot are created by the program AGNOS.

data1.sum Summary file from the first of two data processing programs. DATPRO1. The file contains the unit cell dimensions used for the data processing, background count time, the space group as well as the Laue group no. Summary gives the number of reflections processed and some statistics for the data. The space group extinctions are removed from the data during the processing and the summary shows the average intensity for a space group extinction as well as the maximum value observed for an extinction. The file of space group extinctions is data1.ext.

data2.sum Summary file from the second data processing program, DATPRO2. This file contains the results of the data averaging process. The R for the merging of equivalent reflections is given for all equivelent data and also for the equivalent data that are considered observed.

dis150.inp Input file for the DIS250 program, which calculates the bonded distances and angles as defined in the input file.

four.inp Input file for the Fourier calculation program FOUR.

four.sum Summary file from the Fourier calculation program, FOUR. It contains the max. and min. values of the electron density in the sections.

genles.sum Summary file from the final least-squares refinement cycles. File contains the final R(F), Rw(F), Goodness of Fit, and the maximum value of delta/sigma for the final cycles.

lod.dat File containing information about the data collection parameters. Saved from the PCPS program.

ls.bat Batch file used to run least-squares refinement and difference Fourier calculations.

lsin Input parameter file for the least-squares program GENLES.

lsqpln.sum Summary file from the LSQPLN program. Contains summary of least-squares planes and lines computed for the compound. Also contains interplanar angles. May be saved as a Table(n).

matrix A 3 x 3 matrix used for reindexing data files. When this file is present it is possible that the data was collected using a different unit cell than that ultimately used for the solution and refinement of the structure.

mu.out Output from the Mu program. File contains the contents of Table 1 in the MSC report: Unit cell contents, calculated density for compound, molecular weight as calculated from the formula on the SDT, F(000) and the linear absorption coefficient for the compound.

mu.sum Summary file from the Mu program. (see above)

ortep.inp File containing input instructions for ORTEP-plots. File is created by the plotting program COMM by using the 14 instruction. For organic molecules the file is ready to use, for most other compounds the file will require some editing.

out30 This file is the one used as Tables 3 and 4 in the IUMSC report. It contains the final atomic coordinates, the isotropic equivalent thermal parameter, and their standard deviations. For all atoms refined with anisotropic thermal parameters the anisotropic beta's as well as the U's are given, again with standard deviations obtained from the variance-covariance matrix of the least-squares program, GENLES. Hydrogen atom parameters, idealized or refined are also given.

outda This file contains Table 5 from the report. The table contains all of the bonded distances and angles for the compound, as calculated by the programs DIS250 and DISANG.

outfo This is the Appendix of final Fo and Fc for the structure. The table contains h, k, l, Fo and Fc from the final least-squares refinement, in a condensed format, ready for deposit. Each page contains seven columns each with up to 55 lines, i. e. 385 reflections per page. Note: the F(000) term at the end of the list is not always correct. The F(000) may be defined as the sum of the electrons in the full unit cell. The 'mysterious' characters at the top of the first page are Laser printer instructions.

pksrch.inp Input file for the peak search program, PKSRCH.

pksrch.sum Summary file from the peak search program, PKSRCH. File lists the peaks, their coordinates and peak height.

plots.zip File mainly used by JCH. File contains various input and standard data tape files used for generating the plots in the report. Files can be viewed using PKUNZIP Plots.zip -vn, this gives an alphabetical list of the files contained in the .ZIP. (Files found are SPA.INP, ORTEP.INP, T20A, ANGS.INP etc.)

pubus This file is the anisotropic thermal parameters from the report, (Tables 4a and 4b) without headers. Both beta's and U's are given.

pubxyz This file is the positional parameters from Table 3 in the report without headers. The two 'pub' files are useful for editing for the publication of the structure.

qacell.sum Summary file containing unit cell dimensions with their standard deviations, as determined by a least-squares fit of the setting angles for carefully centered reflections (ANG.DAT). Program used is QACELL.

raw File of raw data for the compound. This file is created from the REF.DAT file. File contains h, k, l, background1, scantime, peakcount, background2, filter # used, sequence #, background time and scan speed.

readme If this file is present, it usually contains remarks regarding problems during the data collection. If the ref.dat file contains bad sections , the README file will show what data lines were deleted during the data processing etc.

ref.dat File containing the data as measured on the diffractometer. This file is written in hexadecimal format, and can be converted to a RAW file using the program PREF. For each reflection the file contains h, k, l, background1, scantime, peakcount, background2, filter no. used, sequence number, background time and scan speed.

report Same as 9nnnn.rep described above.

rs.sum Summary file created during the solution of the structure. It consists of the individual GENLES.SUM files from the sequential runs of GENLES. File usually contains comments inserted by the crystallographer during the solution and refinement process.

sdt21 Output file from the final difference Fourier calculation. This file is the usual standard data tape format. It contains the final atomic parameters plus the peaks located in the final difference map. Note: since this tape is output during the refinement cycles the atoms are not necessarily together.

soln1 Standard data tape of the best solution form MULTAN-78.

spa.inp Input file used for space-filling plots. File is created by the COMM program by using the 11 instruction.

stds File containing the standard reflections measured periodically during the data collection. The standards may be viewed using the program PLTSTDS.

sumry.wp Summary file used in the IUMSC report. If the suffix is .wp, the summary was created using WordPerfect 5.1. If the suffix is .ws (in older reports) it was written using WordStar.

t20 Standard data tape used for input to the least-squares program GENLES. File is not normally saved.

t20a Standard data tape containing the molecule of interest. See 9nnnnA above. This file is used for the ORTEP plots by JCH.

t21 or t21f Final T21 from the least-squares refinement program. Note this tape contains all of the atoms in the asymmetric unit, but are not necessarily together (a flaw in the GENLES program). The atoms can be put together using the SHORTEP program, either by using the BUILD instruction or by suitable 401, 405 and 406 instructions.

t3 Binary file used for by the distance and angle calculation program DIS250. T3 contains the variance-covariance matrix from the least-squares program GEN250 (GENLES). T3 is not normally saved.

t4 Output file from the least-squares progarm GEN250. File is used for creating the Appendix of Fo and Fc, also known as OUTFO or 9nnnn.FO. T4 is not normally saved.

t6 Final data file as used for the least-squares refinement. File contains h, k, l, I, sig(I), scalefactor #, and rho. rho is defined as (sin(theta)/lambda)**2.

t8 Output file from the least-squares refinement program GEN250. Contains data used for calculation of electron density maps. T8 is not normally saved.

t30 Final T30 from the least-squares refinement program, GEN250. This tape contains the final atomic parameters with their standard deviations. This tape is used for generating OUT30, Tables 3 and 4 for the report. Files such as T30A, T30B, etc. are intermediate tapes, they are saved at the convenience of the crystallographer.

t30f Final T30 from the least-squares refinement program, GEN250. This tape contains the final atomic parameters with their standard deviations, and is used for generating tables 3 and 4 in the report.. If the structure has been refined in a 'cyclical' manner the tape will have been put together by the crystallographer.

table(n) Occasionally the report contains additional tables, e. g. least-squares planes, special contact distances, hydrogen bonding etc.

table2a File used by WES for absorption correction data.

tabout This file is Table 2 from the report. It contains details of the data collection, data reduction, experimental set-up, and refinement of the structure.

tape20 Standard data tape used as input file to several programs. It is not normally saved.

tape21 Standard data tape from the final least-squares refinement. This tape contains the coordinates of all atoms in the asymmetric unit put together. This tape is the one used with T30F to create Tables 3 and 4 in the report, it is also the tape commonly listed as Table 6 in the report.

tape22 Standard data tape containing the coordinates of two molecules or fragments fitted together using the BMFIT program. The coordinates of the second molecule are given in the unit cell of the first molecule. When plotted with the COMM program the use of a 13 n instruction will allow the first n atoms to be plotted as a separate unit (usually one molecule in white and the other in red).

tors.sum File containing torsion angles for the compound. Note: As of May 1995 we are not computing standard deviations for the torsion angles.

xtaldt Standard data tape file created by the program AGNOS. It contains the vertices of the crystal shape used for the absorption correction. Can be plotted using ORTEP and the special ORTEP.INP file also created by AGNOS.

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