Douglas Oryx 4 User manual

DouglasInstrumentsLtd.
HardwareManual
Description andConfiguration
Revision5.3,August2006
CompiledbyPatrick ShawStewart,PeterBaldock and JamesSmith
Copyright1991-2006,Douglas InstrumentsLtd.
Douglas InstrumentsLimited
Douglas House ¨East Garston ¨Hungerford ¨Berkshire,RG177HD ¨UK
http://www.douglasinstruments.com

2
Warnings
Always turnofftheMCC and disconnect
thepowercordfromthemainssupply
beforedisassembling anypartsofthe
machineorunplugging theleadsforthe
ChassisorPlateloader
For indooruseonly withinthetemperature
rangeof4-30ºC0-75%RH(Non-condensing)
Oryx ProteinCrystallization machinesare
designedforusewith non-hazardous
matterialsonly.Shouldthe userchooseto
process hazardousmaterialsitwouldbe the
user’sresponsibilitytoobserveanyspecial
handlingprocedures.
The
Red stopbutton
onthe MCCwill
terminateanymovementof theplateloader,
armsandsyringes. Thepurposebeingto
avoidspillageorotherloss ofoil,proteinor
reagents.The machinecomplieswithall
EssentialHealthandSafetyRequirementsof
the EUMachineryDirectiveforCE Marking
Specifications
Power: 100-240 VacUniversalInput; 5A: 50Hz~60Hz
Continuoussound pressurelevelinnormaloperationatthe
operator’sworkstation:below70dB(A) –earprotection neednot
be worn.
Manufacturedby:DouglasInstrumentsLtd.
DouglasHouse,RG177HD,UK
http://www.douglas.co.uk
Type:ORYXCRYSTALLIZATIONMACHINE

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CONTENTS
SETTINGUPTHESYSTEM 4
SoftwareInstallation.................................................................................................................. 4
Layout ofthe Hardware.............................................................................................................4
Recordingthe Positionsof Motors............................................................................................ 5
Unpacking.................................................................................................................................5
ElectricalConnection ................................................................................................................ 5
Installing theZandVArms....................................................................................................... 5
RezeroingMotorizedSyringeDrivers.......................................................................................6
Mounting 100 mlGas-Tight SyringesonMotorizedSyringeDrivers,and
Fillingthem withWater.............................................................................................................. 6
Installing 2.5 mlsyringe.............................................................................................................8
Testing the Performanceof the Plateloader.............................................................................. 9
RealigningthePlateloader........................................................................................................9
Rezeroing all Motorsofthe Plate Loader.................................................................................. 10
FRONTPANELMENU ITEMS 11
USEANDMAINTENANCEOFTHEHARDWARE 15
Installing Microtips.....................................................................................................................15
Use ofLiquidHandling SystemIncluding ValvePositions........................................................15
Refilling100mlGas-TightSyringeswith Water....................................................................... 15
Debubbling ............................................................................................................................. 15
FlushingTubing betweenValves............................................................................................ 16
FillingMicrotipwith Solution................................................................................................... 16
Dispensing Experiments.........................................................................................................16
Attachthe EvaporationshieldforVaporDiffusion Experiments................................................ 17
FlushingMicrotipafterUse....................................................................................................... 18
Alwayswearprotective goggleswhenhandling causticmaterials............................................18
Protein Coatingsof Microtip...................................................................................................... 18
Blockages.................................................................................................................................. 18
ChemicalInertness................................................................................................................... 18
TubingConnections.................................................................................................................. 18
Lubrication of SyringeDrivers andPlateLoader....................................................................... 20
Lubrication of Shafts............................................................................................................... 20
Lead-screws........................................................................................................................... 20
Spillages.................................................................................................................................20
XYZVPlate Loader................................................................................................................... 20
Adjustmentof XYZVPlate Loader.......................................................................................... 20
HARDWARECONFIGURATIONAND CONTROL 21
UsingDifferent Syringeswith the System................................................................................. 21
ChangingPlates........................................................................................................................21
WASPandASPRUN.............................................................................................................. 21
PickAndMix........................................................................................................................... 21
XSTEP– ChangingPlates..................................................................................................... 21
AddingFurtherPlatesto PLATES.DAT.................................................................................... 21
HardwareConfiguration Files.................................................................................................... 22
HARDWARE.CFG.................................................................................................................. 22
HARDWARE.FTH .................................................................................................................. 22
Specifications............................................................................................................................ 24
INDEXOFMANUAL 25

SETTING UP THE SYSTEM
SoftwareInstallation
Followthe instructions inthedocumentontheCD calledInstallation Instructions (Long).rtf
entitled“InstallationofDouglasInstrumentsCrystallizationSoftware”toinstall the
crystallizationsoftware.
Layout oftheHardware
The layoutof Oryx4and Oryx8isshowninthefigurebelow.The systemisdrivenbyaPC,which
isconnectedtotheMCC(MotionControlCenter).The motorizedsyringes andthe XYZV
Plateloaderareinturndrivenbythe MCC using stepper motors. The MCC isacomputerthat
generates thestepsfor thesteppermotors,logs theirpositionsetc. It drivesthemotorsusing 3
DB6steppermotor driver cards.
OryxHardwarelayout

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RecordingthePositionsofMotors
When thesystemisfirst set up, themotorsmustberezeroed usingthe FrontPanel program,as
describedbelow.
Afterthis, the softwarewill automaticallylogthe positions ofallofthe motorsinthe systemand it
will savethesepositions todisk at the endofeachrun. Thismeansthat it isnotnecessaryto
rezerothe motorseach timethecomputerisswitched on. Onlyrezeroifyou havesomereason
tobelievethat thesystemmaybe incorrectlypositioned.However, youmustnot switch off the
computerwithoutquitting allcrystallizationsoftware.If you do this, youwillbeforcedtorezero
the nexttimethat youusethe system.
Unpacking
Take the Chassis, MCC Motion ControlCenter,and theXYZVPlateloader outoftheir packaging.
UnwraptheZ- andV-arms. Take the motorized syringes andground-glass syringesoutoftheir
packaging.
ElectricalConnection
1.Allcablesareindividuallylabeled. Usethe long9-wayD-typecable toconnecttheport
labeled“serialport”ontheMCC totheserialport(COM1)ofthe computer.
2.Followthe labelingtoconnectMCC tothe ChassisandPlateLoaderusingthe three 37-
wayD-type cables
The MCC also possessesoutputsforascreenand keyboard.Thesecan be usedtodiagnose
malfunctions.
InstallingtheZandVArms
NowinstalltheZ-armas follows:
1.UnwraptheZ-arm.
2.Removethe cardboardorplasticprotectivesleeving fromaround theZlead-screw.
3.Lowerthe Z-armintoposition and allowtheleadscrewtosettleonthecentreof the motor
insidetheZV-box.Thearmwillautomaticallybe pulled intothecorrect position onthe
firstrezeroofthetable.
4.Repeatsteps1–3toinstallthe V-arm.

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RezeroingMotorizedSyringeDrivers
1.SwitchontheMCC.Waitforaround20stoallowittofullybootup(Allred and green
lightsshouldgoout). Switchonthehost PC,andallowit tobootup.
2.OnthePC, click onthestart button, then ProgramFiles |DouglasInstruments|Front
Panel.Allow FrontPanel toload.
3.Click on Actions |Rezero.
4.Makesurethat thecheckboxesarechecked forall of thesyringes, and click on continue.
5.If the100 mlsyringes arealreadyinstalled, turnthetop rowofvalves asindicated. Click
Rezero
6.Wait foraround 30seconds whilethesyringedriversmovetotheirlowestpositions.
The motorizedsyringe driversshouldnowbeintheir lowest positions.When theyreach the end
oftheir travel, the syringedriveswill missstepsandmake arattling noise. Thiswillnotharmthe
syringedriversinanyway.Whenyouaresurethat all ofthe syringedrives havereached their
lowestpositions,youcan savetimebyclicking on thelarge red stop button toendthe procedure.
Mounting100 mlGas-TightSyringes onMotorizedSyringe
Drivers,and FillingthemwithWater
1.Prepareabout250mlofdegassed purewater.Thiswillpreventbubblesforming,andis
essentialfor accuratedispensing.
2.Rezerosyringe drivesasdescribed above.
3.PlaceaHamilton Gas-Tightsyringeinpositiononthefirst motorized syringe driver.
Looselyclampthe barrelwiththe barrelclamp.
4.Placethe plunger of thegas-tightsyringe inthe button clamp andtightenthe grub-
screwtofixtheplunger.
Barrelof
gas-
tight
Barrel clamp
Button clamp
Plungerof
gas-tight
syringe
Tighten
grub-screw
Loosely
tighten

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5.Connectthe needleofthegas-tight syringetotheupper valvebypressingtheconnecting
tubing ontoit as far asthegripperfitting.
6.Fill aground-glass syringewithdegassed purewaterand place itinthe femaleLuer
connection on theupper valve.
7.Release the barrel clamp,andremovethebarrel ofthe gas-tightsyringe,leaving the
plungerinposition.
8.Placethebarreloverawastecontainer,andflush all airand bubblesoutofthe
connecting tubingandgas-tightsyringe.Toensurethatno bubblesareleft intheupper
valve, taptheplungerofthe ground glass syringe afewtimes.Flush awayanybubbles
thatappearintothe wastecontainer.
Leaveplungerof
gas-tightsyringe
inplace
Barrelofgas-tight
syringe
Flush barrelusing
ground-glass syringe
Waste
Press the connecting
tubingontoneedleas
far as the gripper fitting
Gripperfitting Fillground-glass
syringewithdegassed
purewater
Uppervalve

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9.Mountthe gas-tightsyringeontothemotorized syringedriverasfollows:
a.Slacken theflangeclamp–labeledbelow
b.Feed the plunger back intothe syringebarrel
c.Placethebarrelintothe Vonthetop ofthesyringe drivernose, ensuringthatthe
flange ofthesyringe barrelisbetweenthenoseand theflangeclamp
d.Tightenthe barrelclamp
e.Tightenthe flange clamp.The flangeclampandthebarrelclampshouldbedone
upfinger-tightonly.
10.Turntheuppervalvetotheflush position ( ),and thelowervalvetothedispense
position(┬). Place awastebeakerunderthelowervalve.Flushair and bubblesoutof
the connectingtubing between the upperandlowervalves.
11.Repeatsteps1-8forthe remaininglowvolumechannels.
Installing2.5mlsyringe
Undothe twoclamps on thelastsyringedriver and installthe 2.5ml syringe.Doupthetwo
thumbscrewstightly.Connectthe correspondingend-fitting tothe last valve.
Flange clamp-
ensure
thatit isunderthe syri
nge
Do upbarrel
clampfinger
-
tight
Do up flange
clampfinger-tight

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Testing thePerformanceofthePlateloader
1.Start Front Panel
2.Click Options | Advanced Menu Items -toturnonAdvanced Menu Items
3.Click Options |AdministratorMode –toturnon Administratormode
4.Click PlateLoader|Diagnostics|TestAxis
5.Set Axis toX, Speedfactor to1.3, Amplitude (mm)to10, Oscillations to10, Placestotest
to5,and Starting at to0.0.Click Test.
6.If thePlateLoadermisses steps,informDouglas Instrumentsofthe problem.Then
reduce the Speedfactor to1.2andrepeatstep 4(again,tryfivetimes). Ifthisfails,
continuereducingthespeed.
7.Followasimilarprocedureforthe Y,Zand Vaxes.If the PlateLoadermisses steps,
reduce thespeed.
8.Click Options |AdministratorMode –toturnoff Administratormode
9.Click Options | Advanced Menu Items -toturnoffAdvanced Menu Items
RealigningthePlateloader
1.Followsteps1-3abovetoturnon Administrator mode
2.Click PlateLoader|ClearTipOffsets -thisclearsanyadjustmentmade tothe tip
position.
3.Install the‘mountedneedle’intothe Z-arm(youshouldfind thisinthered plasticbox)
4.Click PlateLoader|Diagnostics|Align TableandArm…
5.Firstrun the ‘FindIndexPositions’option.–Thiswilljigglethetablemanytimes whileit
finds theoptimumoffsetsforthehomeposition.
6.Nowdo‘Align PointerwithTableDowel’youcanadjustthe tableleft/right.forward/back
toget theneedleinthecentreofthedowel inthe tableThisisastainless pinnearthe 4
screwsinthetable,it shouldbe obviouswhen itgoesthereas it shouldnot be outby
morethan about1.5mm. Ifit isoutbyalot,thePlateloadermayhavehad aheaveknock
duringshipping andthez-boxmayhaveshifted.
7.Do notadjustthe armupanddownatthispoint (you mayusethe‘Lower’ /‘Raise’
buttons, butdon’ttrytomake theneedletouch thedowel using thearrowbuttons)
8.When theneedleiscentered,andwiththearminthe ‘lowered’position,click‘Save’. Add
acommenttothe endofthemessagedisplayedifyou wish.
9.Your tableshouldnowbe aligned properly.

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10.Click Options |AdministratorMode –toturnoff Administratormode
11.Click Options | Advanced Menu Items -toturnoffAdvanced Menu Items
Please note:
When you alignthe tipon the destination plateinan experimentthese offsetsareused on all
otherplates. Ifthe tipisbentandthe endofthetipisfar awayfromthecentreof thecollet
thenit mayappeartobe off centrewhen it loadsprotein.If youlookcloselyyou shouldsee
that theend ofthe tipisinthe centreof the proteintubewhenitstartstogo down,but the
colletmaybe so faroffcentrethatithitsthe side ofthe tube.
It isbesttotrytostraightenthetipbyhand or toadjust thetipintheguideloop tobe pointing
straightdown andinthecentreofthe colletbeforestarting anexperiment.
RezeroingallMotorsofthePlateLoader
1.SwitchonPC andMCC,and start the program FrontPanel as described above.
2. Actions|Rezero. Followinstructions torezeroSyringe Drives,Z,V, XandYmotors.
The Zand Vmotorswillmakealoud rattlingnoisewhentheyarerezeroed.Thisnoise iscaused
bythe motorsmissingsteps. Thiswillnotharmthesysteminanyway. When theloudnoise
startsit canbecut shortbypressingthered StopButton (or byclickingonthered StopButtonon
the screen).
If thisrezeroingroutineisnotcorrectlycarried out, mechanical errorsmayoccur(e.g. themicrotip
maybedamaged,and thegas-tightsyringes maybebroken). However,it needonlybe carried
outduring theinitialsetup,orifthereseemstobean errorwiththemotorpositions.Normallythe
motorpositions aresaved todisk afteruseof the system,andrezeroingisnotnecessary.