Crystal Structure Refinement. A Crystallographer's Guide To SHELXL

232 Pages·2006·2.922 MB·English

by  Muller P. et al

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Crystal Structure Refinement
A Crystallographer’s Guide
to SHELXL
Peter Müller
MassachusettsInstituteofTechnology,Cambridge,USA
Regine Herbst-Irmer
UniversityofGo¨ttingen,Germany
Anthony L. Spek
UtrechtUniversity,TheNetherlands
Thomas R. Schneider
TheFIRCInstituteofMolecularOncology,Biocrystallography,andStructural
Bioinformatics,Italy
Michael R. Sawaya
UniversityofCalifornia,LosAngeles,USA
Editedby
Peter Müller
INTERNATIONALUNIONOFCRYSTALLOGRAPHY
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ISBN-13:978–0–19–857076–9(alk.paper)
ISBN-10:0–19–857076–7(alk.paper)
1.Crystals—Structure. 2.Crystals—Refining. 3.Crystals—Dataprocessing.
I.Müller,Peter,1970–II.Series.
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Foreword
A Short History of SHELX
The 5000 lines of FORTRAN code that became known as SHELX-76 had their
origins around 1970 when the University of Cambridge replaced the ICL Titan
computer with an IBM-370. My previous attempts to write programs used Titan
Autocode,asimplebutefficientprogramminglanguageclosertoassemblerthanto
amodernhigh-levellanguage.WiththeIBMcomputercametwomajorinnovations:
aFORTRANcompilerandpunchedcards.Beingforcedtorewritemyfirstattempt
at a crystallographic least-squares refinement program (called NOSQUARES) in
another language was a good opportunity to learn from my mistakes, but—since
I was too lazy to read the FORTRAN manual or attend a course—I rewrote the
programinaverysimplesubsetofFORTRANthatboreacuriousresemblanceto
TitanAutocode,andavoidedfeaturesthatmighthavebeendifficulttoporttoother
computerssothatIwouldneverhavetorewriteitagain.Thishadtheadvantagethat
itproducedefficientcode,essentialinviewofthelimitedspeedandmemoryofthe
mainframecomputersofthetime(about0.0001timesthatofcurrentPCs).Actually
SHELX-76stillcompilesandrunscorrectlyusingalmostanymodernFORTRAN-95
compiler.
AtthetimeIwouldhaveregardedmyselfasaninorganicchemistwhowasinter-
estedinapplyingavarietyofphysicalmethods;thetitleofmyPh.D.thesis(under
the supervision of Evelyn Ebsworth) was ‘NMR Studies of Inorganic Hydrides’.
When I moved to the Georg-August University of Göttingen in 1978 I discovered
thatmyGermancolleaguesweresomuchbetterat‘cooking’(preparativechemistry)
thanIwasthatitwouldbebetterifIconcentratedoncrystalstructuredetermination,
forwhichtherewasapressingneedinordertocharacterizeallthecompoundsthey
weresynthesizing.
Oneofthemethodswemadegooduseofinthe1960s,forexample,fordetermin-
ingthestructuresofrelativelyunstable-SiH derivativesthathadahabitofexploding
3
in contact with air, was gas phase electron diffraction. This required synthesizing
the compounds in Cambridge and taking them to Glasgow University and later to
UMIST (Manchester) where Durward Cruickshank had the only operational gas
phaseelectrondiffractionmachineinthecountry.OnonevisitImentionedtoDur-
wardthatIwouldneedtodosomeX-raycrystallographybecausenotalloursamples
werevolatileenoughtodeterminethestructuresinthegasphase.Ihadmanagedto
find an X-ray generator and a Weissenberg camera but still needed to write a suit-
able Autocode program for the Titan computer to analyze the data. Durward very
kindly provided me with a set of notes describing least-squares refinement that he
laterpresentedatthe1969computingschoolinOttawa:theseformthebasisofthe
least-squaresrefinementinSHELXtothisday.
vi Foreword
SHELX-76
SHELX was written for use by myself and my students and I never imagined that
it would ever find use outside the ivory towers of Cambridge. However, after a
fewyearsduringwhichtheprogramwasfairlywelldebugged,itbecameclearthat
it would be a good idea to have one definitive ‘export’ version. This was named
SHELX-76andwasintendedtobethefinaldefinitiveversion.SHELX-76included
Lp and absorption corrections for Weissenberg data; in addition to the camera we
hadacquiredaWeissenberggeometrydiffractometerforwhichIwrotethecontrol
program in binary to get the most out of the 4K 12bit words of memory. Fortu-
nately the use of the concept of direction cosines made it possible to handle data
fromothersources.InSHELX-76thiswasfollowedbythemergingofthedatato
produce a list of unique reflections, some primitive direct and Patterson methods
for structure solution, least-squares structure refinement, calculation of dependent
parametersandFouriersyntheses.Theresultingprogramwassolargethatthe5000
FORTRANstatementsweretooheavytocarryaroundasindividualpunchedcards,
soIwrotealittlecompressionprogramfortheFORTRANandanotheroneforthe
testdata(itaveraged9reflectionspercard,i.e∼9bytesperreflection,butcomprom-
ized a little on precision). The program, test data and (uncompressed) FORTRAN
decompressionprogramallfittedintoastandard2000-cardboxthatcouldbeposted
andcamewithmeontripsabroad.Infactthese‘compresseddata’canstillberead
using ‘HKLF 1’ and were subject to a brief renaissance when BITNET was intro-
duced. Once when I was on vacation one of my students dropped the only dataset
fromavaluablecrystalanddistributedthecardsalloverthefloor,butsucceededin
crackingthecodeandputtingthecardsbackintherightorderbeforeIreturned!
One problem that soon became apparent was that the restriction of the array
dimensionstoallowonly160atoms(includinghydrogenatoms)wasalittleonthe
small side; I had thought that this would never need increasing. Dobi Rabinovitch
workedouthowtoincreasethearraystohold400atomsandthisbecamethestand-
ard version. When I was faced with the problem of converting the program to the
first(DataGeneral)minicomputersIwasabletoovercomethememoryrestrictions
(the program and operating system had to fit into 64 Kbytes) by extensive use of
‘overlay’(onlyholdingasmallpartoftheexecutablecodeinmemory)andwitha
ratherefficientblockedcascadeleast-squaresrefinementalgorithmthatrefinedthe
structure in small dynamically selected blocks, but only recalculated the structure
factorcontributionsforatomsthathadchangedinthepreviouscycle.Thiswasthe
basis of the XLS refinement program in the SHELXTL version that I had adapted
forSyntex(wholaterbecameNicolet,thenSiemensandfinallyBruker).XLSonly
fittedintotheNovacomputermemorywithtwobytestospare,sofurtherextension
andevenbug-fixingweredifficult.
SHELX-97
Ilearntagreatdealaboutdirectmethodsofstructuresolutionattheexcellentschools
thatMichaelWoolfsonandLodovicoRivadiSanseverinoorganized,firstinParma
Foreword vii
(1970)andthenfrom1974oninErice.Bythe1980sdirectmethodshadmadesuch
progressthatIdecidedtoproduceaseparatestructuresolutionprogram(SHELXS-
86).ThiswaseventuallyfollowedbyanewrefinementprogramSHELXLin1993,
partly because Syd Hall and the editors of Acta Crystallographica were pester-
ing me to produce CIF output. However CIF is by no means the ideal answer
to the data exchange and archiving problem; even though the CIF file is longer
than the corresponding SHELXL .res file, it lacks much information, for example
about the constraints and restraints applied in the refinement. Both SHELXS and
SHELXLwereupdatedagainin1997andprovedsufficientlyreliablethatnofurther
updateswererequired.Bothprograms(andthesubsequentSHELXC,SHELXDand
SHELXEformacromolecularphasing)weretestedformanyyearsbeforetheywere
released, with the result that they were by that stage already fairly well debugged.
This contrasts with the current general programming philosophy that code is dis-
tributed as soon as possible and the users will find the bugs! This package, which
includedtheprogramCIFTABforworkingwithCIFformatfilesandSHELXPRO
thatactedasaninterfacetothemacromolecularworld,becameknownasSHELX-97.
Documentationisalwaysaproblem,soIsentoutthefirstbeta-testcopiesofthis
package(startingin1992)oneatatime.Apotentialbeta-testerwassentacopyof
themanualandwastoldthatheorshewouldbesenttheprogramsonlyaftersending
meatleastthreeerrorsinthedocumentationorgoodsuggestionsforimprovingit.I
thenmadeallthecorrectionsbeforesendingittothenextguinea-pig.Thefirsttesters
ranitthroughtheirspellingcheckersandfoundplentyofmistakes(myspellingwas
neververygood)butafteracoupleofhundredbeta-testshadbeensentout,people
began to complain that it was all a diabolical plot and that I had simply written
an error-free manual for programs that I had no intention of sending out and that
probablydidn’tevenexist!
Program Style
FewcomputerprogramsoftheantiquityofSHELXareinwideusetoday(though
ORTEP is an even older survivor). One possibility is that the use of a very simple
standardsubsetofFORTRAN,trueevenofthemorerecentadditionstotheSHELX
system, makes it trivial to port the programs to new computer hardware. In com-
parisonwithothercomputerlanguages,FORTRANhasremainedremarkablystable
andupwardscompatible.InthemeantimeIhavelearntsomeCandC++andeven
(severalyearsago)heldPASCALcourses,butconsiderthatFORTRANisstillthe
language of choice for rugged number-crunching programs. FORTRAN shows no
signs of fading out, as exemplified by the excellent selection of FORTRAN com-
pilersavailableforLinuxsystems,andthesheerinertiaofthevastbaseofscientific
FORTRAN code will ensure its survival for a long time to come. There are many
excellentnumericallibrariesavailableforFORTRAN,butIpreferredtowriteevery
line of SHELX myself and did not use these libraries; over the years this has cer-
tainlyenhancedportabilitybecausetheprogramshavenotbecometime-lockedinto
a particular computing environment. The programs are written with (by modern
standards) totally excessive attention to optimizing execution speed and the use
viii Foreword
of memory; a negative side-effect of this is that compiler optimization rarely pro-
duces much improvement in performance. Maybe the spartan programming style,
forexample,therestrictiontoafewsingledimensionarrayswithoneletternames
and the terse comments—originally so that the punched cards could be squeezed
intoonebox—hassimplydeterred‘improvements’totheprogramcode.
The User Interface
An important part of SHELX, and one to which I gave a great deal of thought,
is the user interface. The number of input and output files is kept to an absolute
minimumandtheprogramsusenoconfigurationfilesorenvironmentvariables.So
forastructurerefinement,the(usuallystaticallylinked)executableSHELXLshould
beputsomewhereinthePATHandtwoinputdatafileswiththeextensions.hkl(for
thereflectiondata)and.ins(foreverythingelse)areallthatarerequired.SHELX-76
wasoftenrunfromasinglecard-deckbyconcatenatingthecondenseddatareflection
data (see above) onto the end of the remaining data using ‘HKLF-1’. If one could
find a card-reader, the same card-deck could be fed into SHELXL-97 today and
would produce sensible results. Some users have still not forgiven me for the last
small change I made to the format of the .hkl reflection data file (in 1975). Since
remainingcompatiblehasthehighestpriority,Icouldnotchangethisformatagain
now,thoughitwouldmakeagreatdealofsensetoputtheunit-cellthatcorresponds
totheindexinginthefilebeforethefirstreflection.
The.insinputfilewasdesignedtobeeditedbyhumans,notcomputers.Extensive
useofdefaultvalueskeepsitshort.Defaultvaluesrequirecarefulplanningbecause
theygetused99%ofthetime!FreeformatinputwasararitywhenSHELX-76came
out;itwasnotsupportedbyFORTRAN-66andsohadtobeencodedinFORTRAN,
character by character, but at least this was fully portable. Four-letter words play
animportantrolebothintheSHELXinputandintheEnglishlanguageingeneral!
In addition to the default values, there is also another feature of the .ins file that
makesitverydifficulttoparsewithanothercomputerprogram;tosavespaceIdid
not—like the PDB and other formats—start each atom with ‘ATOM’, so an atom
nameissimplyakeywordthatdoesnothavesomeotherdefinedmeaning.Again,
it would be nice to change this but retaining upwards compatibility is even more
important.
Refinement strategy
MostofSHELXisbasedprimarilyonideasofotherpeople,inparticularusersofthe
program.About90%ofmyowninnovationsthatItriedtoincludeintheprogram
turnedouttobeuseless;Iwascarefultoeradicatealltracesofthesesothatnoone
wouldbetemptedtomisusethem.Thefewinnovationsthatturnedouttobeuseful
instructurerefinementareworthcommentingonhere.Oneofthesewastheintro-
ductionoffreevariables,whichenabledlinearconstraintstobeappliedinasimple
and general way; to do this with other programs often required the user to write a
Foreword ix
special subroutine for each case. Special position constraints were a major applic-
ationoffreevariablesinSHELX-76,bySHELX-97therecognitionandconstraint
of special positions had been fully automated, and the most common application
of free variables today is probably their use to couple the refinement of the occu-
pancies of different disordered atoms and groups. Many other protein refinement
programs still lack special position and occupancy constraints. Rigid group defin-
ition (and the removal of rigid group constraints) is very simple and intuitive in
SHELXL, though the potentially powerful use of quaternions to fit standard frag-
mentstoselectedelectrondensitypeakshasbeenwidelyignoredbyusers.Theuseof
aconnectivityarrayandPARTnumbersprovidesasimpleandeffectiveframework
for defining disorder and generating hydrogen atoms and various restraints; other
macromolecularprogramstendtouseamuchmorecomplicatedtemplateapproach
inwhichallbonds,hydrogenatoms,etc.aredefinedintemplatelibraries(thisiswhy
someproteingraphicsprogramscannotdrawdisulfidebonds!).Theuseofacircular
difference Fourier to find the best positions for hydrogen atoms in -OH and -CH
3
groups was another SHELXL-97 innovation. The ‘similar distance’ restraints and
therestraintsontheanisotropicdisplacementparameters(DELU,SIMUandISOR)
also first came into wide use in SHELXL-97, though the rigid bond restraint was
probably first used by John Rollett. These restraints are essential both for macro-
molecularrefinementandforhandlingdisorder(oftenofsolventmolecules)insmall
molecule structures. I am sure that we will be able to find better ways of restrain-
ing the displacement parameters in the future this was never intended to be the
lastword.
I had never imagined that SHELX would eventually find application in mac-
romolecular refinement, and the introduction of several essential features for this
purposecanbeattributedtoencouragementfromZbigniewDauterandKeithWilson,
whointheearly1990swerelookingforwaystorefineagainsttheveryhighresol-
utionproteinstructuresusingdatacollectedontheEMBLbeamlinesattheDESY
synchrotron in Hamburg. These features included the solvent model (based on the
method used in Dale Tronrud and Lynn Ten Eyck’s TNT program) and conjugate
gradient solution of the least-squares normal equations (as in John Konnert and
WayneHendrickson’sPROLSQprogram).Ididintroducesomeconvergenceaccel-
erationintothisCGLSmethodbytakingintoaccounttheshiftsinthepreviouscycle;
infactCGLSshouldbemorewidelyusedforlargesmallmolecules,itisveryrobust.
HoweverCGLSdoesnotenablethestandarduncertaintiesintheparameterstobe
estimated,soafinalL.S.cycle—usuallywithBLOC1andDAMP00—isrequired
toobtaintheseesdsformacromolecules.ThemostcomplexpartofSHELXLtopro-
gramwasprobablythederivationofstandarduncertaintiesinallderivedparameters
takingallcorrelationtermsfromthefullinvertedleast-squaredmatrixintoaccount.
Onearea,stillneglectedbymacromolecularcrystallographers,istherefinementof
merohedralandnon-merohedraltwins.TestsbyGaribMurshudovandothershave
shown that a significant fraction of structures deposited in the PDB are seriously
in error because twinning had not been taken into account. My colleague Regine
Herbst-Irmermademajorcontributionstothewaysofhandlingandrefiningtwins
withSHELXL-97.