xphelp.docx

xphelp.docx

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xphelp

“HELP”inXP

Type"HELPcommand"tofindoutaboutthefollowingXPcommands:

ARAD,ATYP,BACK,BANG,CELL,CENT,DEMO,DIAG,DRAW,ECHO,EDEN,EGSD,END,ENVI,EXAM,EXIT,EYES,FILE,FMOL,FUSE,GAPS,GROW,HADD,HELP,HIMP,HLPD,INFO,INVT,ISOT,JOIN,KILL,LABL,LIBR,LINE,LINK,LITE,LOSE,MATR,MGEN,MODL,MOVE,MPLN,NAME,NEWM,NEXT,NOPL,OFIT,ORTH,PACK,PAGE,PART,PAWS,PBOX,PERS,PGEN,PICK,POLP,POLY,POST,PREV,PRIN,PROJ,PRUN,PUSH,QUIT,RASD,RAST,READ,REAP,RESI,RIDE,RING,ROTA,SAVE,SFIL,SGEN,SLPF,SLPR,SLXP,SORT,SPIX,SPLT,SPOT,SRCH,SYMM,SYSD,TELP,TITL,TORS,UNDO,UNIQ,USER,VIEW,WAIT,WIPE,ZOOMorthefollowingfacilitiesinXP（firstfourletterssuffice）:

ATOMS,BUGS,COLORS,COMPATIBILITY,ESCAPE,INITIALIZATION,INTERFACE,KEYWORDS,LABELS,NEWS,ORIENTATION,PLOTFILES,SYMCODES

##ARAD

ARADarbrsrkeywords----------------------

Definesatomicradiiforthespecifiedatoms（thatmustbeinthecurrentFMOLlist）.'ar'istheradiusinAngstromsusedforrepresentingtheatomasa（possiblyshaded）circleinTELP,PERS,POLPorPOLYplots.'br'istheradiususedtodefinebondsandisemployedbytheFMOL,SRCH,ENVI,PACK,GROWandUNIQinstructions;theseinstructionsautomaticallygenerateabondbetweentwoatomswhenitisshorterthatbr

（1）+br

（2）+delta,wheretheparameterdeltamaybespecified（thedefaultvalueis0.5）.TheresultingconnectivitytablemaybeeditedusingJOIN,LINK,PRUNorUNDO.'sr'istheradiustobeusedinspace-fillingmodels（SPIXandSFIL）.

The（new）atomname（i.e.elementsymbol）determinesthedefaultvaluesofar,brandsronreadingintheatomsorrenamingthembymeansofPICKorNAME;ongeneratingsymmetryequivalentatomsthecurrentradiiarecopied.TheINFOinstructionlistsatomradiietc.

##ATOMS

ATOMS-----

Anatomnameconsistsofuptofourcharacters,NOTcontaininganembeddedspace,andshouldalwaysbeterminatedbyaspaceortheendoftheline.AtomnamesarerecognisedsimplybyfirstcheckingwhethertheyarelegalXS,XPS,XLorXPinstructions;thusoccasionallyamistypedinstructionmaybemistakenforanatom（itcanbedeletedbyKILLinXP）.

IfanatomwiththesamenameisalreadyintheXPlist,BOTHatomsareretained.Unlesstheyareindifferentresidues,itisadvisabletoavoidthissituation,becauseallsubsequentreferencesapplytoallatomswiththesamename.Ifithappensbyaccident,PICKfollowedbythenameprovidesawaytorenameordeleteoneoftheatomsconcerned.

Onanatominstruction,thenameisfollowedbySFACtype,x,y,z,siteoccupationfactorandeitherU（isotropic）orU11,U22,U33,U23,U13andU12inorder（anisotropic）.AlternativelythesiteoccupationfactorandUmaybeomitted（thedefaultvaluesare1.0and0.05）.TheSFACtypemaybeanynon-zerointeger;ifitisnegative,theabsolutevalueisused.TheSFACtypeisused（togetherwiththeSFACorder）toidentifytheelementwhentheatomisreadfromfile,butthishastobededucedfromtheatomnamewhenanatomisrenamed（NAMEorPICK）.TheSFACtypeisusedforthekeyword'TYPEn'.

TheusualXLconventionsforfixingparametersandtyingparametersto'freevariables'apply,butaredecodedassoonastheatomisreadintoXP.SimilarlyanyMOVEinstructionisappliedONLYtosubsequentatomsread（tomovetheatomsinthecurrentFMOLlistusePUSH）.NotetheuseoftheENVI,SRCH,PACK,UNIQ,GROW,MGEN,PGENandSGENfacilitiesforfindingand/orgeneratingsymmetryequivalentatoms,andNAMEorPICKforchangingatomnames.

##ATYP

ATYPtypecolorkeywords------------------------

Setsthemodeofrepresentationofthespecifiedatoms（thatmustbepresentinthecurrentFMOLlist）inTELPandPOLPplots,andthecolortobeusedinallplots（exceptred-greenstereo）.Forthecolorsavailableandtheirdefaultassignmentsonreadingintheatomssee'HELPCOLOR'.Onreadingintheatoms,'type'issettotheSFACnumber（thatimmediatelyfollowstheatomname）.Theatom'type'hasthefollowingeffectforTELPplots（seePOLPforadescriptionofpolyhedralshading）:

-4:

Dottedellipse（thermalellipsoidboundaryellipse）

-3:

Thermalellipsoidboundaryellipse

-2:

Thermalellipsoidboundaryellipseandprincipalellipses

-1:

Fullthermalellipsoidwithshadedsegments

0:

Nothing（usefulfordummyatoms,e.g.inthemiddleofaC5H5ring）

1:

Shadedcirclewithhighlight

2:

Opencircle

3:

Circlewithregulardotpattern

4:

Circleshadedbottomlefttotopright

5:

Cross-hatchedcircle

6:

Circleshadedbottomrighttotopleft

7:

Circlewithlightrandomdotpatternandhighlight

8:

Circlewithmediumrandomdotpatternandhighlight

9:

Circlewithheavyrandomdotpatternandhighlight

10:

Dottedcircle（usefulforminorcomponentofadisorderedatom）

Theseparationoftheshadinganddotsfortypes1and3-9mayinadditionbevariedbychangingthesecondparameterontheGAPSinstruction.Onreadingintheatomstheyareassignedtypesintherange1-9basedontheatomname;ongeneratingsymmetryequivalentatomsthecurrenttypeiscopied.ItisnotnecessarytouseATYPtoresetallatomtypesinordertoobtainastandardthermalellipsoidplot,sincemakingthesecondparameterontheTELPinstructionnegative（e.g.'TELP0-50'）forcesallatomsexceptHtobeplottedusingtype-1.Thecurrentatomtypes,colorsetc.maybeexaminedusingINFO.

##BACK

BACKcolint------------

Backgroundcolor（anXPcolorindexintherange0-15inclusive）andintensityintherange0（darkest）to3（lightest）forSPIXspacefillingmodels.ThedefaultvalueswillusuallybesetbyaBACKinstructionintheinitializationfilesxtl.ini,butmaybechangedatanytimewithanewBACKinstruction.

##BANG

BANGkeywords-------------

BANGprintsallinteratomicdistancesspecifiedinthecurrent（FMOL）connectivitytableforeachatomdefinedbythe（BANG）keywords,plusallanglesinvolvingtwosuchbondswithanatomincommon.Thetypeofbond（assetbyLINKorJOIN）makesnodifference.

##BUGS

TherearenoknownbugsinSHELXTLrelease5.02!

ForinformationaboutbugsthatwereeliminatedinthisreleaseseetheNEWShelpfile.

##CELL

CELLlambda,a,b,c,alpha,beta,gamma----------------------------------------

CELL（usuallyreadfromthe.resor.insfilebyREAD）followedbysevennumbersinputsthecrystallographicunit-cellandreinitialisesallstructuralparameters（exceptTITL）.

CELLfollowedonlybylambda（thatmaybegiventhearbitraryvalue1）signalsthatallfollowingatomiccoordinatesrefertoaunitorthogonalsystem;freevariablesetc.maynotthenbeused（butMOVEisallowed）,andinstructionsimplyingcrystallographicsymmetryorcrystalcoordinates（e.g.LATT,SYMM,FILE,SRCH,ENVI,SGEN,UNIQ,GROW,POLP,POLYandPACK）arenotpermitted.

CELLwithnoargumentscausesthecurrentcelltobeprinted.

##CENT

CENTkeywords-------------

Thex,yandzcoordinatesofthe（unweighted）centroidofthespecifiedatomsarecalculated.ThisissometimesusefulinconjunctionwiththeOFITinstruction,e.g.tofitthecentersoftwoaromaticrings.

IfCENTisfollowedimmediatelyby/X（withoutaninterveningspace）,anatomofATYP0withthecalculatedcoordinatesisaddedtotheFMOLlist,butnobondsareaddedtotheconnectivitytable.Thisisusefulforpi-bondedorganometalliccomplexes;allthatremainsistobondthe（dummy）atomtothemetalatom（JOIN3or4）andthenPERSorTELPmaybeusedimmediately.InsuchacaseFMOLshouldbeavoided,becauseitwillgeneratetoomany'bonds'.

##COLOR

COLORS------

codemonitorinkjetpenplottersuggesteduse

0brownblackblackbonds

1greengreengreenF,Al,Ni

2darkredredredFe,Br,Pt

3darkblueblueblueCo

4yelloworangeorangeS,Na,Fourierpeaks

5purplemagentapurpleP,K,Mn

6whitelightgreengreen*H（*turquoisefor8-penplotters）

7graygrayblackC（*blackforPERSandSPIX）

8bluecyanblueD,N,Ru,Ag

9darkgreengreengreenCl,others

10lilacpurplepurpleLi,Cr,I

11orangeorangeorangeB,Sn,Au

12turquoiselightcyanblue*Cu,Si,Os（*turquoisefor8-pen）

13brownbrowneorangeSe,Sb,Mo

14darkgraygrayblackAs,Hg

15redredredO

Plotterpensshouldbeinsertedinthefollowingorder（notethatthisisdifferentfromtheorderinversion4ofSHELXTL,toconformwithHPandMicrosoft）:

Black,red,green,orange,blue,purple,（turquoise）,（none）.

ColorsarespecifiedbymeansofATYPinstructions,andareignoredwhenproducingred-greenstereoplots.Theprogramusestheabovelisttosetdefaultcolorsonreadingintheatoms.Plotfilesalwaysincludecolors,butmaybeplottedinblackandwhitewithe.g.RAST/L,or'1'inanswertotheDRAWquestionaboutthenumberofplotterpens.

##COMP

COMPATIBILITYOFXPFILESBETWEENOPERATINGSYSTEMS

IngeneralallASCIIfilesreadorwrittenbyXParecompatibleoverdifferentoperatingsystems,e.g.onaNFSsharednetwork.IngeneralALLSHELXTLprogramsonbothMSDOSandUNIXsystemscanreadeitherDOSorUNIXformatASCIIfiles（orevenmixedformat!

）.Insomecasesfileprotectionproblemsmaymakeitnecessarytocopyorchmodafilebeforeitcanbeaccessedbyanothercomputeronasharednetwork.

AlthoughSHELXTLplotfilesarebinary（whichmakesthemmuchmorecompact）theycanbereadandwrittenbyXP（andwrittenbyXPREP）onallplatformssupportedbySHELXTL.Thenecessaryrecorddelimeters,bytereversaletc.arehandledinternallybytheprogramandrequirenospecialactionbytheuser.ThusforexamplethePC,SGIandRS/6000versionsofSHELXTLcanallaccessthesameplotfilesonadisksharedusingNFS.Notethatinversion5ofSHELXTLtheformatisthesameforal