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Welcome to the Help Desk.

This page contains helpful How-to-do pamphlets, Practical materials, Hints and tricks and other suggestions that may make your crystallographic projects a little easier.

Professional Help (all Texas A & M Students, Staff and Faculty)

For Instrument Repair or Usage Questions follow this link >>  Instrument Help

 

Brief Introduction to X-ray Powder Diffraction [pdf][html]

 

Brief Introduction to Single-Crystal Diffraction

 

SHELX-CARD PDF (SHELXL-97)

SHELX-CARD PDF (SHELXL-2013)

SHELX-CARD EPUB (SHELXL-97)

SHELX-CARD EPUB (SHELXL-2013)

SHELX-CARD MOBI (SHELXL-2013)

JANA page flip manual (Václav Petříček & Michal Dušek)

 

Class Periods Texas A & M University

Deposit CIF to CCDC

 

Get Help

Our staff is available to assist you with your structure (at any stage).  There is no charge for Texas A & M University users, for all other users please contact us for information.  Please follow the steps outlined below for assistance.

Step one : Complete the Help Desk Worksheet

We will require, the full data set, structure information, user information and a brief description of the problem. 

Step two : Please compose an e-mail and send this information and the Help Desk Worksheet with the attached data (zipped if necessary).

Step three : We will examine your problem as time permits. 

Please E-MAIL us first before your office visit!  This will allow us some time to exam your problem and schedule a time to discuss it with you.

Please do not come to our offices WITHOUT the Help Desk Worksheet and the structural information!

Unannounced office visits will not speed up the process and will result in lost time and productivity!

Your problem may require many hours of work so please be patient.

X-ray Diffraction is an analysis tool for solid crystalline, semi-crystalline and amorphous materials.  Before you begin you should have a basic understanding of the principles of X-ray Diffraction and Crystallography.  There are many good courses available at Texas A & M University and on-line Tutorials (see Tutorials).

  • TAMU Users
  • Academic Users
  • Commercial Users

Two general methods to acquire research information are available to you

1) You may submit a sample to us for investigation

2) You may collect your own data.

If you choose option two then you must first be qualified to use the instrumentation, undertake safety training and go through instrument usage training.

You are qualified to use the instrumentation if you are an employee of Texas A & M University and are covered by workman's compensation insurance.

Visiting researchers are generally covered.  Please check with your principle investigator to be sure.

See NEW USERS for full details.

We have been partially funded by the National Science Foundation

Academic users should submit samples to us in person or by post. 

Users are encouraged to follow the steps outlined in the sample submission section of this web site.

We will gladly work with all commercial users. 

Please see the user All Users section of this web site for more details. 

Users are encouraged to follow the steps outlined in the sample submission section of this web site.

 

Frequently asked questions

Table of Contents

Basic Questions

What is X-ray Diffraction?
Why do you use X-rays?
Why do you use crystals?
How do you determine molecular structure from X-rays and Crystals?
What are crystal lattices and the unit cell?
What are the Bravais Lattices?

What is a Space Group?

Local Question (for Laboratory users)
How and where to submit samples
To reserve instrument time you must...
How much will it cost?
Do I you need general X-ray safety training YES IF ..
What free crystallographic programs do I need to get started ...
If the X-ray lab collects my data and I want to solve and refine my structure ...
How do I access the Cambridge Data Base?
I  need help on solving and/or refining my structure

General Questions
How do I grow good crystals?
How do I mount my sample?

Odds and Ends

Historical
Must Read Book List for Crystallographers

Crystallographic References





Basic Information


 

Xray Diffraction is ..

X-rays scatter off of electrons, in a process of absorption and re-admission.  Diffraction is the accumulative result of the x-ray scattering of a group of electrons.  For an incident X-ray photon of monochromatic wavelength ?, coherent waves are produced at an angle of theta (2-theta with respect to the incident x-ray) if the electron groups interact with the x-ray and are spaced at a distance d.  The interaction is described by Bragg's law : nlamda =2dsin(theta).  The intensity of the scattered x-ray is proportional to the number of electrons that the x-ray is scattered from.

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We use X-rays because ...

Normally one would use a microscope to view small objects. For a microscope, light is scattered by an object and collected using lenses, which in turn magnifies the image of the object. The limit of the microscope is intrinsic to the nature of the electromagnetic radiation that is used to probe the object.   If we use light we cannot look at objects smaller than the wavelength of light which is about 10 -6 m.  Since the atom has dimensions of about 10-10 m we cannot image an atom with a photon of light.   X-rays, on the other hand, have a wavelength of about 10 -10 m and are suitable for imaging objects at the atomic scale.

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We use crystals because ..

To observe a single object, we normally fix the object to a microscope slide.  To view an atom we would need some method to handle a small atom and align it in the microscope.  This would be quite difficult and the x-rays scattered by a single atom is extremely week.  A better method is to use 1020atoms (the number found in a small -crystal) and to sum the scattered x-rays from each atom.  The trick is to align the atoms in neat orderly rows and columns so that the scattered x-rays would form predictable patterns that are based on the original arrangement of the atoms.  All of the atoms of a single-crystal are oriented the same way and the scattered x-rays are superimposed and can be measured.   Each scattering event that is measures is called a "reflection". There is typically 2000 to 100000 independent reflections for each single-crystal.

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We can determine Molecular Structure ....

The scattered x-rays contain both angular and intensity information.  The information concerning the position of the electrons (and atoms) involves both the amplitude and phase of the scattered intensities.  For standard data collection techniques the amplitudes for the diffracted intensities are measured, however the phases are lost due to the nature of the experiment.  Direct methods is employed to re-determine the phases. 

Structure determination is the process of model building, structural factor (intensity) prediction and comparison to the observed structure factors.  The model is constructed by introduction of atomic positions at electron density maxima.  The model is then employed to predict structural factors which are refined (non-linear least squares) against the observed structural factors.  The comparison between the predicted and observed structure factors is known as the residual and attests for the validity of the model.

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Crystal Lattice and the unit cell are ...

A single-crystal is described as an order set of atoms (electrons) in a fixed orientation.  Typically a single crystal suitable of analysis is at least 50 µm in its smallest dimension and not more than 500 µm in its largest.   The smallest non-reproducible volume of the crystal is called the unit cell. The size of the unit cell ranges from a few hundred cubic angstroms (10-10 m) to 10's of thousands.  By application of symmetry the unit cell can be repeated, in three dimensions, to describe the entire crystal.   The unit cell in turn can be described by three non-coplanar axis a, b and c and the inter axis angles alpha ,beta and gamma which are called the Lattice Parameters.    Seven crystal systems are described in terms of the lattice parameters

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The seven crystal systems are

 

SYSTEM UNIT   CELL   LENGTH UNIT  CELL  ANGLES
1) Cubic a = b = c alpha=beta=gamma=90deg
2) Tetragonal a = b      alpha=beta=gamma=90deg
3) Orthorhombic no conditions alpha=beta=gamma=90deg
4) Rhombohedral a = b = c alpha=beta=gamma does not equal 90deg
5) Hexagonal a = b alpha=beta=90deg   gamma=120deg
6) Monoclinic no conditions alpha=beta=90 deg
7) Triclinic no conditions no conditions

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The Bravais Lattices are ...

Lattice Symbol
1) Primitive P
2) (single face centered cells)
     A face (bc plane) - centered A
     B face (ac plane) - centered B
     C face (ab plane) - centered C
3) Face - centered F
4) Body - centered I

 

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Space Groups are ...

Space groups are a way of describing how objects are arranged in three-dimensional space.  There are four symmetry operations allowed in  three dimensional "space". 

 

Operation Symbol (Hermann) Symbol (Schoenflies)
Rotation 1,2,3,4,6 E, C2, C3, C4, C6
Reflection m Cm
Inversion -1, 2/m i
Rotation/Inversion -1,-3,-4,-6 n/a

A symmetry operation followed by translation is also allowed

 

Screw axis       21, 31, 32, 41, 43, 61, 65

Glide planes    a,b,c,n,d

 

A space group is described as a closed set of symmetry operations that describe the total symmetry of a given volume of space (unit cell).  The first letter of the space group describes the centered cell (P, A, B, C, F or I).  The following symbols represent the smallest set of non-reducible symmetry operations. 

e.g.       Pmmm     Primitive cell with three perpendicular mirror planes

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Local Questions

 


How and where to submit samples

Submit your samples to the X-ray staff for approval.  Bring your sample to rm 2409 between 9:00am-5:00pm weekdays

There are two ways to submit your sample and determine your structure.

 
1st ) You can request that the x-ray diffraction laboratory staff undertake the investigation.  
    This way is suggested if ...
    a) you undertake only a few structural determinations a year
    b) your advisor does not want you to undertake the time and expense of learning a new skill.

 
2nd ) You can be trained and you can do your own work.  This method is suggested  if ...
    a) your structures are major part of your research
    b) you must defend your structures before skeptical investigators

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To reserve instrument time ...

 
If you choose for the x-ray diffraction laboratory staff to do your structure or powder diffraction experiment then we will reserve time for you.  If not you should reserve time on one of the three CCD diffractometers, the GADDS diffractometer, the D8 discover, the D8 vario or the SAXS instrument

 
To reserve time please use the calendar reservation system.

See the x-ray diffraction facility manager for the SAXS reservation.

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How much will it cost?

See Fees.  For Industrial users please call 979-845-9125 or e-mail.  

For Industrial users please call 979-845-9125 or e-mail.

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Yes you need safety training IF ...

Yes !! :  If you intend to do your own structures

No      : If you wish for the staff to do your structures

X-ray Safety Training

Before you begin the x-ray staff will train you on the site specific safety issues. 

Goto NEW USERS page for further details.

For more general x-ray safety training you will be expected to attend one of the classes presented by the Environmental Health and Safety Department (EHSD).  Their training schedule can be found here :     General X-ray Training

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Free crystallographic programs to get started ....

You should download some of the free crystallographic software on the net

     a)WinGX -  A GUI (windows) for some of the most popular (and free) software.  First download the software and then e-mail the author for a free license.   SHELXS, SHELXL, PLATON, SIR92 and several other valuable programs come with the package.

     b)GTREP - A structure graphics and plotting program.  Will plot thermal ellipsoids.

     C)Mercury from the CSD

See Crystallographic Program Guide

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If the X-ray lab collects the data we will provide ..

You will be given (at least) two files    project_name.HKL and  project_name.INS  with these files and WinGX you can solve refine and display your structure.     The X-ray Staff will assist you the first few times.

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The Cambridge Crystallographic Data Base can be ..

 
The Cambridge Crystallographic Data Base is located on a PC computer RedHat Linux E5 (xray.chem.tamu.edu) and can be accessed by here

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You can get help with your structure.  Goto the Helk Desk on this site


 

General Questions

 


How do I grow good crystals?

Crystals :  See Growing Crystals

Recommended reading
P.G. Jones: Crystal growing, Chemistry in Britain (1981) 17, 222-225. 
J. Hulliger: Chemistry and Crystal Growth, Angew. Chem. Int. Ed. Engl. (1994) 33, 143-162. Angew. Chem. (1994) 106, 151-171. 
A. Holden, P. Morrison: Crystals and Crystal Growing, MIT Press, Cambridge, Massachusetts (1982) ISBN 0-262-58050-0 
J.W. Mullin: Crystallization, Butterworth-Heinemann, Oxford, Great Britain (1993) ISBN 0-7506-1129-4 

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How do I mount my sample?


Two methods are commonly employed.
    a)Thin glass fiber
A thin glass fiber is pulled and attached to a copper pin (magnetic base, Hampton) with clay and finger nail polish.  The fiber can be pulled by heating a Klimax® melting point tube in a hot flame.  The fiber is typically 50 to 100 mm in diameter.  The crystal is glued to the fiber with an adhesive.

    b)Nylon loop
A thin (thickness  = 20mm) 0.7 mm diameter nylon loop  (Hampton) that is attached to a magnetic base is coated with Paratone®  or Apieazon® grease is used to "lasso" (Texas style) a crystal and pulled it off the microscope plate. 

Hints 

-Crystals can be covered with a thin layer of oil to prevent decomposition in air.  
  Mineral oil.  
  Paratone® (a poly-isobutylene:  additive free STP)
  Poly-isobutylene (is available in several viscosities)
  Perfluorinated oils (Krytox® oil)
  Epoxy resin (less hardener)
  Apieazon® grease

-If your crystals lose solvent, try adding a few drops of the solvent (mother liquor) to mineral oil or paratone and then cover the crystals with this mixture.  Some experimentation on solvent concentrations in the oil may be needed.

-Adhesives for specimen pins
  super glue                holds up to 373K       dries fast
  dental cemen                        to 573K        dheres to glass well
  Epoxy resins                         to 373K        slow drying
  Apiezon® Grease(T)               to 103K       slow scatter
  Silicon Grease (not 4)             to 133K       Si scatter (cheap)
  Vaseline                               to 200K           sticky
  Balsam                                 to RT         dilute with xylene)
  Wax                                     to RT           permanent

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Crystallographic Papers


Historical Papers

Birth of Crystallography :   

1669 Nicolaus Skno :  Determined that angles between crystal faces remained constant between crystals of the same compound.

1895 Rontgen :  Discovers X-rays : Science (1896) 53, 274. (in English)
First X-ray Diffraction Experiment :   Friedrick, W. Knipping, P. & Laue, M.  Bravarian Acad. Sci. (1912) 303. 
First Structure Determination : Bragg, W.H & Bragg W.L. Proc. Royal. Soc. (1913) A88, 428.
First X-ray Camera (Powder): Debye, P. & Scherrer, P. Phys Z. (1916) 17, 277-283.
                                         Hull, A. W.  Phys. Rev. (1917) 10, 661-696.
First X-ray Diffraction Instrument: Weissenberg, K. Z.Phys. (1924) 23, 229.
First Geiger Counter:  Locher, G.L. & LeGalley, D.P. Phys. Rev. (1933) 46, 1047.
First X-ray Precession Instrument : Buerger, M.J. "X-ray Crystallography"  (1942) Wiley, New York
First Scintillation Counter: West, H.I., Mayerhot, W.E., Hotstadter, R. Phys. Rev. (1951) 81, 141.

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Top Ten Must Read Crystallographic Books.


1. Crystal structure determination  by: Werner Massa                  
      "My favorite introduction to Crystallography"
     "It's the one book I would force into a student hands!"
2. Crystal Structure Analysis by: Glusker and Trueblood
     "A good starter for the common scientist"
3. Crystal Structure Determination  and Crystal Structure Analysis  by: Bill Clegg
     "One of my favourite and informative book(s).  First time crystallographers should read these books first."
4. Cystallography Made Crystal Clear   by: Gale Rhodes 
      "For the Novice/macromolecular user"
5. Fundamentals of Powder Diffraction and Structural Characterization of Materials by: Pecharsky and Zavalij
    "Only book that I know of that explains indexing and indexing programs"
    "A must own book for the powder and single-crystal diffractionist!"
    "A gota-have book for people interested in the bigger picture"
6. Structure Determination by X-ray Crystallography by: Ladd and Palmer 
        "I have given Ladd and Palmer to non-crystallographers who needed to gain 
         a basic understanding of the process."
7. X-ray Structure Determination by: Stout and Jensen 
       "a good, practical book for the student after they are into the subject" 
8. X-ray Analysis and the Structure of Organic Molecules by: Dunitz 
           "a great book (even for an inorganic chemist) and it is filled Jack's usual wit"
           "The section on weighting schemes in least squares is a must read"
9. The Determination of Crystals Structures by: Lipson & Cochran
           "It is still an amazing book!"
10. Fundamentals of Crystallography  edited by C. Giacovazzo
            "A MUST HAVE for a lab"
           "For more advanced students Giacovazzo is a must."

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References

Absolute Configuration

 
Absolute Configuration
Jones, P.G. (1986) Acta Cryst.A42, 57-57. 

Flack absolute structure
H.D. Flack (1983) Acta Cryst.A39, 876-881 
G. Bernardinelli and H.D. Flack (1985) Acta Cryst.A41, 500-511. 
H.D. Flack and G. Bernardinelli (2000) J. Appl. Cryst.  33, 1143-1148.

Rogers absolute structure 
Rogers D. (1981) Acta Cryst.A37 734-741. 
Jones P.G. (1984) Acta Cryst.A40, 660-662. 

Hamiltons' R-test 
Hamilton, W.C. (1965) Acta Cryst.18, 502-510. 

Alternative to Hamitons' R-test 
Rothstein, S.M. ; Richardson, M.F. and Bell, W.D. (1978) Acta Cryst.A34, 969-974

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Absorption

 
Absorption Coefficients 

International Tables for Crystallography, Volume C (1992), Ed. A.J.C. Wilson, Kluwer Academic Publishers, Dordrecht: 4.2.4.2 (pp. 193-199).

Absorption Correction 

Blessing, R.H. (1995) Acta Cryst. A51, 33-38. 

Azimuthal only (no theta dependence) 

North A.C., Philips, D.C. and Mathews, F. (1968) Acta Cryst .A24, 350-359. 

Azimuthal + theta correction 

Flack, H.D. (1974) Acta Cryst. A30, 569-573. 

Analytical 

DeMeulenaer, J. and Tompa, H. (1965) Acta Cryst. 19, 1014-1018. 
Katayama, C. (1986) Acta Cryst. A42, 19-23. 

Numerical 

Busing, W.R. and Levy, H.A. (1957) Acta Cryst. 10, 180-182. 
Coppens, P., Leiserowitz, L. and Rabinovich, D. (1965) Acta Cryst. 18, 1035-1038. 

Statistical 

Katayama, C. (1972) Acta Cryst. A28, 293-295. 

Difabs 

Walker, N. and Straurt, D. (1983) Acta Cryst. A39 158-166. 

XABS2 

Parkin, S.; Moezzi,B. and Hope, H. (1995) J.Appl.Cryst. 28, 53-56. 

Sperical 

International Tables for X-ray Crystallography, Vol II. Birmingham; Kynoch Press., Tables 5.3.6B pages 302-305.

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Tests for Center of Symmetry

Wilson, A.J.C. (1949) Acta Cryst., 2, 318-321. 
Howells, E.R.; Phillips, D.C. & Rogers D. (1950) Acta Cryst., 3, 210-214. 
Marsh, R.E. (1986) Acta Cryst., B42, 193-198. 

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Crystallographic Information File

CIF format :: I.U.Cr. Commission on Crystallographic Data:
S.R. Hall, F.H. Allen and I.D. Brown (1991) Acta Cryst., A47, 655-685. 

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Chemical Group Modeling


Ipso-angles of phenyl rings differ systematically from 120 degrees 

P.G. Jones (1988) J. Organomet. Chem., 345, 405 
T. Maetzke and D. Seebach (1989) Helv. Chim. Acta, 72, 624-630 
A. Domenicano, "Accurate Molecular Structures", eds. Domenicano and Hargittai, Chapter 18, OUP (1992) 

Standard (restraint) bond lengths based on the CSD 

F.H.Allen, O. Kennard, D.G. Watson, L. Brammer, A.G. Orpen and R. Taylor in Sections 9.5 and 9.6 of Volume C of "International Tables for Crystallography" (1992), Ed. A.J.C. Wilson, Kluwer Academic Publishers, Dordrecht, pp. 685- 791.

Standard (retraint) bond lengths for protiens 
R.A. Engh and R. Huber (1991) Acta Cryst., A47, 392-400. 

Standard (restraint) bond lengths For nucleic acids 
R. Taylor and O. Kennard (1982) J. Mol. Struct., 78, 1-28 (bases and phosphates) 
S. Arnott and D.W.L. Hukins (1972) Biochem. J., 130, 453-465 (furanose rings). 

Plainarity of nucleic acid bases 
R. Taylor and O. Kennard (1982) J. Am. Chem. Soc., 104, 3209-3212 

Diffuse solvent modeling by Babinet's principle 
R. Langridge, D.A. Marvin, W.E. Seeds, H.R. Wilson, C.W. Hooper, M.H.F. Wilkins and L.D. Hamilton (1960) J. Mol. Biol., 2, 38-64
H. Driessen, M.I.J. Haneef, G.W. Harris, B. Howlin, G. Khan and D.S. Moss, J. (1989) J. Appl. Cryst., 22, 510-516 

Rigid body analysis 
Schomaker, V. and Trueblood, K.N. (1968) Acta Cryst., B24, 63-76.

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Data Collection and Reduction

Area Detection -CCD strategies
S. Ruhl and M. Bolte (2000) 215, 499-509

Area Detection -peak bases
Bolotovsky, R.; White, M.A.; Darovsky, A. and Coppens, P. (1995), J. Appl. Cryst. 28, 86-95. 

Diffractometer 
Alexander, L & Gordon S.S. (1962) Acta Cryst., 15, 983-1004. 

Diffractometer Alignment 
Samson, S. and Schuelke, W.W. (1967) Rev. Sci. Instr., 38, 1273-1283. 

Cell reduction and Lattice Symmetry 
Glegg, W. (1981) Acta Cryst., A37, 913-915. 
Gruber, B. (1973) Acta Cryst., A29, 433-440. 

Scan type Wyckoff 
Wyckoff, H.W.; Doscher, M.; Tsernoglou, D.; Inagami, T.; Johnson, L.; Hardman, K.D.; Allewell, N.M.; Kelly,M. & Richards, F. (1967) J. Mol. Biol., 27, 563-578.

Data Reduction 
Blessing, R.H. (1987) Cryst. Rev., 1, 3-58. 
Blessing, R.H. & Langs, D.A. (1987) J.Appl. Cryst., 20, 427-428. 

X-ray beam and Detection 
Harkema, S.; Dam, J.; Van Hummel, G.J. and Reuvers, A.J. (1980) Acta Cryst., A36, 433-435. 
Katrusiak, A. & Ryan, T.W. (1988) Acta Cryst., A44, 623-627. 
Nelson, J.T. & Ellickson, R.T. (1955) J. Am. Opt. Soc., 45, 984-986. 

Intensities 

Slaughter, M. (1968) Kristallogr., 129, 24-35. 
McCanlish, L.E.; Stour. G.H. and Andrews, L.C. (1975) Acta Cryst., A31, 245-249. 
French, S. & Wilson, K. (1978) Acta Cryst., A34, 517-525. 

Learnt Profile Analysis 

Diamond, R. (1969) Acta Cryst., A25, 43-55. 
Clegg, W. (1981) Acta Cryst., A37, 22-28. 

Lehmann/Larsen method 

Lehmann, M.S. & Larsen, F.K. (1974) Acta Cryst., A30, 580-584. 

Floating Baseline 

Reibenspies, J.H. (1994) J.Appl.Cryst. 26,426-430. 

Normal Back/Peak/Back 

Tickle, I.J. (1975) Acta Cryst. B31, 329-331. 

Slope Detection method 

Grant, D.F. & Gabe, E.J. (1978) J.Appl. Cryst. 11, 114-120. 

Misc. procedures and investigations 

Spencer S.A. and Kossiakoff (1980) J. Appl. Cryst., 13, 563-571. 
Dudka, A.P. and Loshmanov, A.A. (1992) Sov. Phys. Crystallogr., 36, 625-626. 
Langford, J.L. (1978) J. Appl. Cryst., 11, 10-14. 
Lehmann, M.S. (1975) J. Appl. Cryst., 8, 619-622. 
Chulichkov, A.I.; Chulichkova, M.; Fetisov, G.; Pyt'ev,Y.P.; Lupyan, Y.V.;Laltionov, A.V.; Nesterenko, A.P. and Aslanov, L.A. (1987) Sov. Phys. Crystallogr., 32, 649-653.
van der Wal, H.R.; de Boer, J.L. and Vos, A. (1979) Acta Cryst., A35, 685-688. 
Strel'tsov, V.A. and Zavodnik, V.E. (1989) Sov. Phys. Crystallogr., 34, 824-828. 
Norrestam, R. (1972) Acta Chem. Scand., 26, 13-21. 
Rigoult, P. J. (1979) J.Appl.Cryst., 12, 116-118. 
Blessing, R.H.; Coppens, P. & Beker, P. (1972) J. Appl. Cryst., 7, 488-492. 
Rossman, M.G. (1979) J. Appl. Cryst., 12, 255-238. 

Reflection Intensity Photography 

Xuong, N. & Freer S. Acta Cryst., B27, 2380-2387. 

Laue Film Integration & Deconvolution 

Shrive, A.K.; Clifton,I.J.; Hajdu, J. and Greenhough T.J. (1990) J. Appl. Cryst., 23, 169-174. 

Decay Correction 

Abrahams, S.C. and Marsh, P. (1987) Acta Cryst., A43, 265-269. 
Ibers, J.A. (1969) Acta Cryst., B25, 1667-1668. 



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Extinction Correction

 
A.C. Larson in "Crystallographic Computing" (1970), Ed. F.R. Ahmed, Munksgaard, Copenhagen, pp. 291-294. 
Larson, A.C. (1967) Acta Cryst., 23, 664-665. 
Zachariasen, W.H. (1963) Acta Cryst., 16, 1139-1144. 

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Least Squares Refinement

Floating origin restraints: 
H.D. Flack and D. Schwarzenbach (1988) Acta Cryst., A44 499-506. 

Use of all data in refinement. 
F. L. Hirshfeld and D. Rabinovich (1973) Acta Cryst., A29, 510-513 
L. Arnberg, S. Hovmoller and S. Westman (1979) Acta Cryst., A35, 497-499 

Refinement of racemic twins 

Pratt, Coyle and Ibers (1971) J. Chem. Soc., 2146-2151 
Jameson (1982) Acta Cryst., A38, 817-820. 

Conjugated Gradient L. S. algorithm 

W.A. Hendrickson and J.H. Konnert "Computing in Crystallography", Ed. R. Diamond, S. Ramaseshan and K. Venkatesan, I.U.Cr. and Indian Academy of Sciences, Bangalore 1980, pp. 13.01-13.25.
D.E. Tronrud (1992) Acta Cryst., A48, 912-916. 

Least-Squares Restraints : 

J.S. Rollett in "Crystallographic Computing", Ed. F.R. Ahmed, S.R. Hall and C.P. Huber, Munksgaard, Copenhagen, (1970) pp. 167-181.
F.L. Hirshfeld (1976) Acta Cryst., A32, 239-244 
K.N. Trueblood and J.D. Dunitz (1983) Acta Cryst., B39,120-133. 
.J. Didisheim and D. Schwarzenbach (1987) Acta Cryst., A43, 226-232 

Shift limiting least-squares restraints (damping) Marquardt algorithm :: 

Marquardt (1963) J. Soc. Ind. Appl. Math., 11, 431-441. 

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Program References

 
SHELXTL-PLUS

Sheldrick, G. (1990) SHELXTL-PLUS revision 4.11V, SHELXTL-PLUS users manual,Siemens Analytical X-ray Inst. Inc., Madison WI, U.S.A.

SHELXS-86 

Sheldrick, G. (1986) SHELXS-86 Program for Crystal Structure Solution, Institüt für Anorganische Chemie der Universität, Tammanstrasse 4, D-3400 Gottingen, Germany.

SHELXL-97

Sheldrick, G. (1997) SHELXL-97 Program for Crystal Structure Refinement, Institüt für Anorganische Chemie der Universität, Tammanstrasse 4, D-3400 Gottingen, Germany.

TEXSAN

teXsan : Single Crystal Structure Analysis Software, Version 1.6 (1993). Molecular Structure Corporation, The Woodlands, Texas 77381.

DIRDIF-99

Beurskens, P., Admiraal, G., Beurskens G., Bosman, S., Garicia-Granda, R., Gould, J., Smykalla, A. and Smykalla, C. (1992). DIRDIF-99 program system, Technical Report of the Crystallography Laboratory, University of Nijmegen, The Netherlands

SIR-97

Giacovazzo C. (1997) SIR-97 Program for Crystal Structure Solution, Inst. di Ric. per lo Sviluppo di Metodologie Cristallograpfiche, CNR, Univ. of Bari, Italy.

SIR-88

SIR88 : Burla, M.C.; Camalli, M.; Ccascarano, G.; Giacovazzo, C.; Polidori, G. and Viterbo, D. (1989) J. Appl. Cryst. 22, 389-393.

PATSEE 

Egert, E. (1985) PATSEE Program for Crystal Structure Solution by Integrated Patterson and Direct Methods, Institüt für Anorganische Chemie der Universität, Tammanstrasse 4, D-3400 Gottingen, Germany. Egert, E. and Sheldrick, G. (1985) Acta Cryst A41, 262-268.

SHAKAL

SCHAKAL88 : Keller, E. (1989) J. Appl. Cryst. 22, 12-22. 

PLUTON

Spek, A.L.. (2002) PLUTON. Program for Molecular and Crystal Graphics. Vakgroep Algemene Chemie, University of Utrecht, Afdeling Kristal-En Structuurchemie, Padualaan 8, 3584 Ch Utrecht, The Netherlands.

PLATON
Spek, A.L.. (2002) PLATON. Program for Crystal Structure Results Analysis. Vakgroep Algemene Chemie, University of Utrecht, Afdeling Kristal-En Structuurchemie, Padualaan 8, 3584 Ch Utrecht, The Netherlands.

ORTEP-76

Johnson, C.K. (1976) ORTEP-II. A Fortran Thermal-Ellipsoid Program, Report ORNL-5138. Oak Ridge National Laboratory, Oak Ridge Tennessee.

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Space groups/ Laue symmetry / Unit cell

polar space groups 
H.D. Flack and D. Schwarzenbach (1988) Acta Cryst., A44 499-506 

MISSYM 
LePage, Y. (1987) J Appl. Cryst., 20, 264-269 

Lattice symmetry determination 
Mighell, A.D. and Rodgers, J.R. (1980) Acta Cryst., A36, 321-326. 
Baur, W.H. and Tilmanns, E. (1986) Acta Cryst., B42, 95-111. 


Structure inversion for special space groups 
E. Parthe and L.M. Gelato (1984) Acta Cryst., A40, 169-183 
G. Bernardinelli and H.D. Flack (1985) Acta Cryst., A41, 500-511

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Statistical Descriptors in Crystallography

D. Schwarzenbach; Abrahams, S.C.; Flack, H.D.; Gonschorek, W.; Hahn, T;Huml, K.; Marsh, R.E.; Prince, E.; Robertson, B.E.; Rollet, J.S. and Wilson, A.J.C. (1989) Acta Cryst., A45, 63-75.

 

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Twinning

Racemic twinning 
H.D. Flack (1983) Acta Cryst., A39, 876-881. 

Twinning structural reasons. 
W. Hoenle and H.G. von Schnering (1988) Z. Krist., 184, 301-305. 
Buerger, M.J. (1945) J. Am. Miner., 30, 469-482.

SHELXL-97
R. Herbst-Irmer, G. Sheldrick (1998) Acta Cryst, B54, 443-449. 

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Weighting Scheme

Statistical bias 

A.J.C. Wilson (1976) Acta Cryst., A32, 994-996. 

Exponential weights 

J.D. Dunitz and P. Seiler (1973) Acta Cryst., B29, 589-595. 

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X-ray flux

Honkimaki, V.; Sleight, J. and Suorott, P. (1990) J. Appl. Cryst., 23, 412-417. 

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ShelX help

ShelX-97 manual
Shelx-Cards reference
XP-instructructions reference

ShelX-97 Flip Book

ShelX - Guide (Gregory S. Girolami, Julia L. Brumaghim, James G. Priepot, and Jon P. Goveia)

References

William Clegg and David G. Watson (2008) Acta Cryst. E64, e15-e17.

ABSCOR:
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.

APEX, APEX2, SMART, SAINT, SAINT-Plus:
Bruker (2007). Program name(s). Bruker AXS Inc., Madison, Wisconsin, USA. [Older versions (pre-1997) should refer to SiemensAnalytical X-ray Instruments Inc. instead of Bruker AXS.]

CAD-4 Software:
Enraf–Nonius (1989). CAD-4 Software (or CAD-4 EXPRESS). Enraf–Nonius, Delft, The Netherlands.

Cambridge Structural Database:
Allen, F. R. (2002). Acta Cryst. B58, 380–388.

CAMERON:
Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON.Chemical Crystallography Laboratory, Oxford, England.

CrysAlis CCD, CrysAlis RED and associated programs:
Oxford Diffraction (2006). Program name(s). Oxford Diffraction Ltd,Abingdon, England.

CRYSTALS:
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin,D. J. (2003). J. Appl. Cryst. 36, 1487.

COLLECT:
Nonius [or Hooft, R.W.W.] (1998). COLLECT. Nonius BV, Delft, The Netherlands.

DENZO/SCALEPACK:
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.

DIAMOND:
Brandenburg, K. [or Brandenburg, K. & Putz, H., or Brandenburg, K.& Berndt, M.] (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany.

DIF4 and REDU4:
Stoe & Cie (1991). Program name(s). Stoe & Cie, Darmstadt, Germany.DIRAX:
Duisenberg, A. J. M. (1992). J. Appl. Cryst. 25, 92–96.

enCIFer:
Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M.(2004). J. Appl. Cryst. 37, 335–338.

EVALCCD:
Duisenberg, A. J. M., Kroon-Batenburg, L. M. J. & Schreurs, A. M. M.(2003). J. Appl. Cryst. 36, 220–229.

JANA2000:
Petrˇıcˇek, V. & Dusˇek, M. (2000). JANA2000. Institute of Physics, CzechAcademy of Sciences, Prague, Czech Republic.

Mercury:
Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P.,Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39,453–457.

Mogul:
Bruno, I. J., Cole, J. C., Kessler,M., Luo, J., Motherwell,W. D. S., Purkis,L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E. & Orpen, A. G. (2004). J. Chem. Inf. Comput. Sci. 44, 2133–2144.

ORTEPII:
Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak RidgeNational Laboratory, Tennessee, USA.

ORTEPIII:
Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL- 6895. Oak Ridge National Laboratory, Tennessee, USA.

ORTEP-3:
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.

PARST:
Nardelli, M. (1995). J. Appl. Cryst. 28, 659.

PLATON:
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.

PROCESS:
Rigaku (1996). PROCESS. Rigaku Corporation, Tokyo, Japan.

PROCESS-AUTO:
Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan.

publCIF:
Westrip, S. P. (2008). publCIF. In preparation.

SADABS, TWINABS:
Bruker (2001). Program name. Bruker AXS Inc., Madison, Wisconsin,USA.
or
Sheldrick, G. M. (1996). Program name. University of Go¨ ttingen,Germany.
All programs beginning with SHELX:
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

SIR92:
Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla,M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.

SIR97:
Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo,C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999).J. Appl. Cryst. 32, 115–119.

SIR2002:
Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103.

TEXSAN:
Molecular Structure Corporation & Rigaku (2000). TEXSAN. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.

WinGX:
Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.

X-AREA, X-RED, X-RED32, X-SHAPE:
Stoe & Cie (2002). Program name(s). Stoe & Cie, Darmstadt, Germany.

XCAD4:
Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.

XSCANS:
Siemens (1994). XSCANS. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.

X-SEED:
Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191

Crystallographic Databases available for TAMU domain users.

  • Cambridge CSD
  • Inorganic ICSD
  • Powder ICDD
  • Misc. Databases

The Cambridge Crystallographic Data Base is available on line see WebCSD.


A copy is also located on a windows computer in room 2409.

 

 

The Inorganic Crystal Structure Database


The icsd data base is available on-line see ICSD

You must enter the data base from the .tamu.edu domai

The International Centre for Diffraction Data 


Powder Diffraction database.

The Department of Chemistry presently owns the 2004 license.  This is restricted to data base searches with the program EVA.

See the database manager for details.