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IUMSC   Indiana University Molecular Structure Center

Keep in mind that the Reciprocal Net servers are research support tools for collaborators of the crystallography laboratories that run them. For that reason, most of the nearly 6,000 compounds are unusual or unique materials that could only be characterized by using X-ray diffraction techniques.

In addition to the structures that are being examined as part of ongoing research programs, a collection of "common molecules" is available. This collection (currently 300+ structures) has been designed primarily for educational use and is located on the Reciprocal Net master server (http://www.recipnet.org). The common molecule server uses a different view for each entry as shown below.


molecule view from common molecule server (Click to see an enlarged image)


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EXAMINING STRUCTURES

Once a data entry has been located by using one of the available search techniques, the data entry pages (see Crystallographic Data Access page) can be used to view the structure and examine the data tables. In order for any of the JaMM applets to work properly, there must be a file nnnnn.crt present in the directory. This file consists of labels, Cartesian coordinates, and the atomic number for each atom to be plotted, and a bond pair table that indicates which of the atoms are connected. For entries added after January, 1999 the .crt file also contains symmetry information. If this file is present, the JaMM applets (MiniJaMM, JaMM 1 and JaMM 2) can be used to view the molecule. If you select a data entry that does not display the molecule in any of the JaMM applets, check to see that a .crt file is present (look in the report and data files link on the data entry page.

If the nnnnn.crt file is present and correct, you will be able to use any of the JaMM applets, and generate the rendered images using JaMM 1 and JaMM 2. In order to view ORTEP style drawings, two additional files must be present in the directory. The first of these is the nnnnn.sdt file, the "standard data tape" format that is used by the Reciprocal Net. The .sdt contains the coordinate data in crystallographic coordinates, not Cartesian coordinates. In addition it contains symmetry information, scattering factors, and other specialized data used by the various programs in the IUMSC XTEL library. If the nnnnn.sdt file is present along with a shortened ORTEP input file called nnnnn.ort, the ORTEP Drawing option will work (assuming the two files are correctly formatted). In general, each data entry is checked to insure that the files are correct.

It should be emphasized that the ORTEP drawings are dependent on the contents of the two files mentioned. If molecular symmetry is present, the files will be created to contain one complete molecule. If cations and anions are present, the file may or may not reflect this fact. Solvents located in the crystal lattice are generally not included in the .sdt and .ort files, even if they are important to the crystal packing. An attempt is made to include a "complete" .crt file (nnnnnf.crt) which has all atoms present in the cell (even disordered atoms). Recent structure will also have a .pdb file present (nnnnn.pdb). This file is also a Cartesian coordinate file in a form recognized by the RasMol graphics software and the Chime plug-in. If the .pdb file is not present, a utility program is available to convert .crt files to .pdb files.

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CRYSTALLOGRAPHIC DATA FILES

In addition to the files needed for molecular visualization, there are usually a number of files present that are of use primarily to the crystallographer or the collaborator who is publishing the structural data. The following describes some the files that may be present and their contents:

  • nnnnn.cif
  • nnnnn.crt
  • nnnnnrep.pdf
  • nnnnnrep.doc
  • nnnnn.da
  • nnnnn.doc
  • nnnnn.fo
  • nnnnn.ort
  • nnnnn.rep
  • nnnnn.sdt
  • nnnnn.t21
  • nnnnn.tab
  • nnnnn.txb
  • nnnnn.txt
  • nnnnn.us
  • nnnnn.xtel
  • nnnnn.xyz
  • nnnnnlb.zip
  • mol.gif
Crystallographic information file
IUMSC Cartesian coordinate file (described above)
pdf version of final report
Word version of final report
Table listing bonded distances and angles
Word document giving summary information
Listing of observed and calculated structure factors
ORTEP input file (described above)
Complete printable report (for hp printers-PCL formatting)
IUMSC standard data tape (described above)
Final data tape from last XTEL least squares run.
Crystal data file shown on data entry page
duplicate of .tab file--internal use
ASCII text version of nnnnn.doc file
Thermal parameters for atoms
Present on older structures--same as nnnnn.crt
Fractional coordinates for atoms
All files in compressed format (PKZip)
Thumbnail image of molecule

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