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

Notes

Space Groups
Big 5 Spacegroups
Little 5 Space Groups
Frequency

Solvents and Ions
c6h12
c6h6
ch2cl
ch2cl2
ch3cn
ch3oh
common_ions
dioxane
solvents
thf_solvent
electron

Math/Figures of Merit
fom.pdf
Imaginary Numbers
Guinier Equation Solved
hieroglyphs
note_imaginary_numbers

Meetings
reibenspiess_ppxrd
ecm_2004_reibens

Miscellaneous
sucrose
sugar_crystals

User Manuals (all are freely avialable on the web)

apexiiusermanual
bis_op
brukerd8advtutorial
bruker_apex_install_linux_redhat
bruker_guide
cameronusersmanual
cell_now
cifguide
cifreferencemanual
cosmo
crunch
cullite_stock_references
d4manual
detectordistancebeamcenter
dirdif
error_codes
evasearchcomplete
expo
fit2d_intro
fit2d_ref_10.3
gadds
gaddsmanuall
gaddsquickguide
gemanual
GGCS commands
kristalflex
kryoflexmanual
kyroflex2
kyroflex_french
liebert
Lytron_startup
manual-RC006-RC045-G02-820-0043
manual_jana98
nanostar
news_letter_blurb
oxford
oxford_lt_probe
patsee
phihome1000
platon
platon_flipper
platon_twinning
pluton
primus
prot
RADIATION SAFETYTRAINING GUIDE 441-1-12
rasmol
REGULATORY GUIDE 08-029
rlatt_help
rotax
sadabs
saxsdatacollection
service-chiller-maint-930-0011[1]
service-clean-pdp-strainer-930-0006[1]
service-maintenance-pdp-820-0148[1]
sfactableforshelxcu
sfactableforshelxmo
shelx-de
shelx
shelxd
shelxtl_nt
Shelx_97
sir92
sir97
smart_troubleshooting_manual
struplo
topas
twinabs
upgradingbruker-axscomputers
usermanagerusermanual_04
vncforwindows
wingx
winplotr_epdic
xdb
xpcommands
xraylec
xraysafety
xshellover
xshellquickhelp
xshell_tutor
xshell_users
xtalgrow

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.

 

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)