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Crystalographic Library

This page contains reference material for crystallographic studies.

For structure help see the helpdesk page.

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

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

access to the Cambridge Crystallographic Database is available on line : WebCSD


Also a copy is located on a RedHat Linux E5 (xray.chem.tamu.edu) server and can be accessed by

a) Windows (XP and 20000)
        You will need the program X-WIN 

            LiveCD (will not work with VISTA) see :  CSD for Windows

                When prompted type ssh -X xray.chem.tamu.edu and then login

b) Linux
        at prompt type ssh -X xray.chem.tamu.edu

c) A Silicon Graphics Computer, access the same as Linux

d) Macintosh access the same as Linux.

Notes :  Login accounts and passwords are available to qualified users contact the database manager for details

To start the database type   "cq"  at the Linux prompt.

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.

 

Crystallographic Slang.

Feel free to contact us with new definitions or corrections

A+B structure: A chemist being asked what the compound is expected to be answering – I do not know, I simply reacted A and B and got these crystals!
bananas – Term used to describe unusually long (prolate) thermal ellipsoids (see cigar, eye sore).
blob - An apparently solid substance with faces that turns out to be amorphous.
boulder -  A well-formed crystal that is much too large and will need to be cut. (see rock, honker)
brick- A large crystal (see boulder, rock, honker).
burn – To expose to X-rays
canned - To stop a data collection on a crystal because the structure is not wanted.
carriage return structure: A routine structure based solely on default values but coming out perfectly
chimney sweep brush- similar to starburst
cigars - Term used to describe unusually long (prolate) thermal ellipsoids (see bananas, eye sore).
cooked - To accidentally warm a crystal to room temperature (see fried).
crunch – An extended structure solution session.
dandelion head - see starburst
deck of cards - A crystal that consists of multiple lamellae.
diffracts like a b*tch - a large crystal of known structure, which you keep handy to put on in order to convince a student that it is indeed their sample and not your instrument which is the problem, without first having to switch off the Cryostream to mount the test crystal.
digger – An individual who will not give up looking for crystalline samples at the expense of other people.
dust – Very small particles often mistaken for single-crystals.
eyesore – A structure with poorly shaped structural parameters.
feed the bulldog - To generate sufficient revenue (results) to meet expenses (expectations).
fish eggs - round glassy gels. Usually balls of silicone grease.
fisher – An individual who spends an extended time on the microscope searching for crystal samples (see digger).
fishhook - A curved needle crystal
flick - To remove a crystal from it's mount because it is of insufficient quality (see ping).
flipped – To solve a structure with a charge flipping algorithm.
footballs - See bananas
free lunch - Procedure for padding data with extra information.
fried – To accidentally warm a crystal to room temperature (see cooked).
friend – An extrusion growth or secondary crystallite on a main crystal (see fuzz).
frisbee– Term used to describe unusually flat (oblate) thermal ellipsoids (see pancakes, eye sore)
fuzz – Small randomly orientated crystals.
fuzzball - A round blob of crystalline material that consists of very thin needles growing from a common center.
gear grinder – An individual who misuses an instrument.
glass – A non-crystalline solid often mistaken for a crystal.
grind – An extended structure refinement.
honker – Large well formed crystals (see rock, boulder)
house brick - similar to rock.
igloo – Term used to describe the appearance of a specimen when the LT is not working properly (see snowball).
instant death – Crystals that instantly decay when exposed to air.
jello - more blocky fish eggs.
juice - X-ray flux (intensity) : as in "we need to get more juice out of the tube for this crystal"
kaput - A term used to describe a dead crystal, instrument or project.
lead on a stick – A mounted crystal with very high absorption coefficient.
marshed – To be cited by R. E. Marsh for extraordinary contributions to the crystallographic literature. To be cited for employing questionable symmetry assignments.
moly or molly – Molybdenum radiation X-ray tube.
NBG – No bloody good.
nirvana - Checking the crystal status or mounting a new one after 10 p.m.
nuke - To deliberately remove a crystal from a mounting pin.
one-crystal yield - The smallest possible nonzero yield when using single-crystal X-ray diffraction methods.
pancakes – Terms used to describe unusually flat (oblate) thermal ellipsoids (see frisbee, eye sore).
passer – An individual who repeatedly starts a project but cannot finish it and passes it to someone else (see team player)
piggy backing – The act of using an instrument after someone else has finished their data collection, but before the next reservation, thus collecting a data set at no cost to piggy backer.
ping - To remove a crystal from it's mount because it is of insufficient quality (see flick).
pseudo-crystal -  A solid bit in the bottom of the flask that looks like a crystal, rotates polarized light like a crystal, and doesn't have a diffraction pattern.
quantum crystal - A crystal that mysteriously appears and is accidentally employed in a data collection.
rock – Large well formed crystals (see honker, boulder)
rugby balls - See bananas
SCS - sh***y crystal syndrome
SDS - sh***y data syndrome
sea anemone – Small crystalline needles that share a common point in space (see star burst)
shoot – To expose to X-rays (see burn, zap)
SIS - sh***y instrument syndrome.
sludge – A non-viscous non-crystalline liquid often mistaken for a crystal.
snap - see burn
snowball – Term used to describe the appearance of a specimen when the LT is not working properly (see igloo).
SOS - sh***y operator syndrome.
squashed – A crystal structure where electron density has been over subtracted from void space.
squeaker – An individual or group too cheap to pay for a crystal structure.
squeezed – A crystal structure where electron density has been subtracted from void space.
squozed – A crystal structure where electron density has been mistakenly subtracted from void space
sea urchin - see star burst
star burst – Small crystalline needles that share a common point in space.
sweater fuzz - An unexplained solid mass that is mistaken for your sample (see fuzz).
surfboards - See frisbees
team player – An individual who believes that every other individual is on their team and that each member of the team has their own duties.
thumper – An individual repeatedly reserves time on an instrument, exams a few specimens and then releases that time so that they will not be charged.
time bandit – An individual who wastes another individual’s work time.
to hit with a hammer– A brute force approach to structure solution (see TREF 2000).
TREF 2000 – A brute force approach to structure solution (see to hit with a hammer).
whale – A very large structure.
X-believer – A person who is convinced the single crystal system is not working properly because he cannot get a unit cell on his bad crystals:
X-calibrator – A former collaborator who finds another crystallographer because they do not believe a crystal structure determination.
X-pectator – A person who expects too much from the crystal structure analysis
X-peter – An individual who repeatedly collects data on bad crystals.
X-tension - Elemental analysis by crystallographic methods.
zap – To expose to X-rays (see burn, shoot)
zeppelin - Term used to describe unusually football (american) shaped thermal ellipsoids (see cigars)
zinger – Structural results the contradict the original chemical diagram.

Book List

Proofiness: The Dark Arts of Mathematical Deception by Charles Seife (isbn: 0670022160 )

There are two Errors in the Title of This Book by Robert M. Martin (isbn: 1551114933)