iMosflm-tutorial

iMosflmtutorial1.Introduction1.1BackgroundMOSFLMcanprocessdiffractionimagesfromawiderangeofdetectorsandproduces,asoutput,anMTZfileofreflectionindiceswiththeirintensitiesandstandarddeviations(andotherparameters).ThisMTZfileispassedontootherprogramsoftheCCP4programsuite(POINTLESS,SORTMTZ,SCALA,TRUNCATE)forfurtherdatareduction.TheMOSFLMprogramwasoriginallywrittentoprocessdatacollectedonfilm.ItwasthenmodifiedtoprocessdatacollectedusingtheimageplatedetectordevelopedattheEMBLoutstationinHamburgbyJulesHendrixandArnoLentfer,andthenamewaschangedtoipmosflm.Thisisthecurrentversionoftheprogram,whichwillalsoprocessdatafromCCDandpixeldetectors.1.2InstallationThenewGUI(imosflm)iscurrentlyavailableforWindows,MacOSXandLinuxplatforms.AFordetailsofinstallationvisit(mosflm_user_guide.txt)orontheweb()asaPDForHTMLdocument.ItisaverygoodideatolookthroughthisguidebeforestartingseriousdataprocessingwithMOSFLM,althoughyoudonotneeditforthistutorial.1.Theon-linehelp.IfyoutypehelpattheMOSFLM=prompt(afterstartingtheprogram)allpossiblekeywordsarelisted,withinformationoneachkeyword.Thisinformationisstoredinanasciifile(mosflm.hlp)whichcanalsoberead(andsearched)withaneditor.ThisreliesonhavingtheenvironmentvariableCCP4_HELPDIRsettothedirectorycontainingthisfile.ThisisalsoavailableontheMOSFLMwebpagesunderkeywordsynopses2.1.4AimsofthetutorialYourtaskistoprocess84images,hg_001.mar1600tohg_084.mar1600,collectedonaMar345imageplatedetectoratasynchrotronbeamline.Thesearecrystalsofasmalldomain(91aa)thathavebeensoakedinamercurycompound,resultinginadatasetwithastronganomaloussignalwhichcaneasilybeusedtosolvethestructure.TheseimageshavekindlybeenprovidedbyCamilloRosano.2.OverviewofiMosflmStarttheprogrambytypingimosflm.Afterabriefdelay,thefollowingwindowwillappear:iMosflmTutorial1of3118/05/1014:18Thebasicoperations(Images,Indexing,Strategy,CellRefinement,Integration,History)canbeselectedbyclickingontheappropriateicon,butthosethatarenotappropriatewillbegreyedoutandcannotbeselected.2.1DropDownmenusClickingonSessionwillresultinadropdownmenuthatallowsyoutosavethecurrentsessionorreloadapreviouslysavedsession(oraddimages):ClickingonViewwillallowyousee(andmodify)ExperimentSettingsorProcessingoptions.Thesewillbedescribedlater.iMosflmTutorial2of3118/05/1014:18ThethreesmalliconsbelowSessionallowyoutostartanewsession,openasavedsessionorsavethecurrentsession.Movingthemouseovertheseiconswillresultindisplayofatooltipdescribingtheactiontakeniftheiconisclicked.3.AddingimagestoasessionToaddimagestoasession,usetheAddimages...icon:Selectthecorrectdirectory(thedefaultisthedirectoryinwhichimosflmwaslaunched)fromthepopupAddImageswindow.Allfileswithanappropriateextension(whichcanbeselected)willbedisplayed.Doubleclickingonanyfilewillresultinallimageswiththesametemplatebeingaddedtothesession(thetemplateisthewholepartofthefilenameexceptthenumberfieldthatspecifiestheimagenumber).(AnalternativeistosingleclickandthenclickonOpen)Thephivaluesforalltheimages(readfromtheimageheader)willbedisplayedintheImagewindow.AllimageswiththesametemplatebelongtothesameSectorofdata.Multiplesectorscanbereadintothesamesession.Eachsectorcanhaveadifferentcrystalorientation.NotethataWarninghasappeared.ClickanywhereinthewarningsboxtogetabriefdescriptionoftheiMosflmTutorial3of3118/05/1014:18warning.Inthiscase,itisbecausethedirectbeamcoordinatesstoredinMarimageplateimagesarenottrustedbyMOSFLM,andthedirectbeamcoordinateshavebeensettothephysicalcentreoftheimage.Clickonthecrossontherighthandsidetoturnoffthiswarning.Thedirectbeamcoordinates(readfromtheimageheaderorsetbyMOSFLM)andcrystaltodetectordistancearedisplayed.Thesevaluescanbeeditediftheyarenotcorrect.AdvancedUsageThephivaluesofimagescanbeeditedintheImagewindow.Doubleclickwiththemouseoverthephivaluestomakethemactive,allowingnewvaluestobegiven.Thesenewvaluesarepropagatedforallfollowingimagesinthesamesector.1.Todeleteasector,doubleclickonthesectornametoselectit,thenusetherightmousebuttononthesectortobringupadeletebutton.Movethemouseoverthedeletebuttonandreleasetherightmousebuttontodeletetheimages.2.Ifonesectorisaddedandusedforindexing,andthenasecondsectorfromthesamecrystalisadded,thematrixforthesecondsectorwillnotbedefined.Todefineit,doubleclickonthematrixnameforthefirstsector,saveittoafile,doubleclickonthematrixname(Unknown)forthenewsectorandreadthematrixfilewrittenforthefirstsector.3.4.ImageDisplayWhenimagesareaddedtoasession,thefirstimageofthesectorisdisplayedinaseparateDisplaywindow.TheImagedropdownmenuallowsdisplayofthepreviousornextimageintheseries.TheViewdropdownmenuallowstheimagetobedisplayedindifferentsizes(relatedbyscalefactorsoftwo),basedontheimagesizeandtheresolutionofthemonitor.iMosflmTutorial4o