MX2 Full User Manual - Australian Synchrotron
Contents
1. STALLOGRAPHY JSER SUPPORT STAFF Beamline Speed dial 8540 4123 8540 4120 0434 307 453 a 8540 4187 2synchrotron org au 0488 342 426 lt 2 8540 4295 nchrotron org au nicliffe 0408 574 371 3 0419 351 988 4 rt Officer 8540 4136 nchrotron org au 0423 823 985 5 rt Officer 8540 4112 tron org au 0429 028 938 6 rt Officer I O tron org d u Document AS OAM 0001 Created by Ruth Plathe2. O 1 Y _ Australian Synchrotron DA SX LIOS OTT UT gt Roe Q CRYSTALLOGRAPHY MICRO BEAMLINE MX2 USERS MANUAL Contents MX2 User Manual 1 0 Personnel Safety System PSS 2 0 Chemical Biological and Cryogenic Safety 3 0 Beamline User Resources at the Synchrotron 4 0 Beamtime Preparations 4 1 Mounting Samples Manually 4 2 Using the Stanford Automated Mounting SAM System 4 3 Sample Preparation AS Cassette Kit 4 3 1 Dewar Shipping 4 4 Remote Experiments 4 5 Remote Experiment Support LOGRAPHY BEAMLINE MX2 Page 2 Contents MX2 User Manual 5 0 Beamline Computer System Blu Ice 5 1 Log Tab 5 2 User and Staff Tabs 5 3 Hutch Tab 5 4 Sample Tab 5 5 Collect Tab 5 6 Scan Tab 6 0 Beamline User Resources around the Synchrotron 6 1 Food 6 2 Computer and Electronics Supply Stores 7 0 Map of Facility 8 0 Key Services Locality Map Clayton Back page Contact Details for MX Beamline Staff F Page 3 LOGRAPHY BEAMLINE MX2 1 0 PERSONNEL SAFETY SYSTEM PSS Inside the hutch i Strobe Will flash while siren is sounding Alerts the users to leave the hutch i Siren When the search button is l I pressed the siren will sound until the search and secure process is either finished or aborted There are 3 different sirens one when the search is in progress another to indicate the I I
3. e The label on the smallest circle corresponds to the lowest resolution to which data will be collected e The Vertical and Horizontal positions of the detector see Adjusting Detector Position section can also be used to determine the amount of detector offset you may require Any movement of these positions will also be updated automatically on the Resolution Predictor The Hutch Tab allows the users to adjust various parameters for data collection by entering the desired values into the input boxes found in the Hutch Overview menu If changes cannot be made the input box is grayed out or inactive and hovering the mouse over the input box will return an error message The changes are shown in red and are not made until the Move button is pressed Hitting the Cancel button restores the edited motor values to their current position Hitting the Abort button will stop the changes while they are being made In general all motors will remain at the position at which the Abort button was pressed Note hitting Abort more than once is likely to crash the Blu Ice and or detector servers 5 4 SAMPLE TAB Mounting with the Robot Interface The interface in the Sample tab may be used to mount crystals one at a time using the Stanford Automated Mounting SAM robot You must have already organised for your user support staff member to load your cassette s into the robot dewar inside the hutch before you begin Using this interface does not nec
4. 003 phi 0 3 deg wedge 5 deg 2 energies inverse beam off Two or more Energies Inverse Beam On Phi Two or more Energies Inverse Beam On Phi Wedge Wedge Size Size example test 1 E1 001 test 1 E1 002 test 1 E1 003 test 1 E1 181 test 1 E1 182 test 1 E1 183 test 1 F2 001 test 1 E2 002 test 1 E2 003 test 1 E2 181 test 1 E2 182 test 1 E2 183 phi 0 3 deg wedge 5 deg 2 energies inverse beam on example test 1 E1 001 test 1 E1 002 test 1 E1 181 test 1 E1 182 test 1 E2 001 test 1 E2 002 test 1 E2 181 test 1 E2 182 test 1 E1 003 test 1 E1 183 test 1 E2 003 test 1 E2 183 phi O 3 deg wedge 2 deg 2 energies inverse beam on ALLOGRAPHY BEAMLINE MX2 Page 30 Run Sequence The run sequence depends on the values for phi wedge energy or inverse beam that you choose The image collection order will be displayed in the run sequence window Note Once the current run is finished the software will go on to collect any unfinished runs following the current one 5 6 SCAN TAB The Scan Tab is used for energy and excitation scans There are two modes from which to choose e Excitation Scan mode is used to identify and verify GST ru3 1 047 GST ru3 1 052 GST ru3 1 053 GST ru3 1 054 GST ru3 1 058 GST ru3 1 059 GST ru3 1 060 GST ru3 1 061 GST ru3 1 062 GST ru3 1 063 GST ru3 1 064 GST ru3 1 065 GST ru3 1 066 GST ru3 1 067 GST ru3 1 068 GST ru3 1 069 G
5. AS has common waste streams on site please seek advice before your arrival Biological Safety i Nitrile gloves and safety glasses are required when working with I I l l i biological samples Users are responsible for the safe labeling and I disposal of their own biological samples Page 6 TALLOGRAPHY BEAMLINE MX2 AL 3 0 BEAMLINE USER RESOURCES SYNCHROTRON SUPPLIED Cryogenic tools LA durable foam rubber dewar that holds 800 ml of liquid nitrogen is provided at the beamline These are manufactured by Spear Labs They are easier to handle and safer to use than a traditional low profile glass Dewar Also because of its lower thermal mass a foam vessel will cause less liquid nitrogen boil off when it is filled ELLEN MD MP DI lI The long CrystalWand is a 205 mm chrome plated steel wand 9 6 mm in diameter with a magnet molded inside one end The CrystalWand has a plastic handle i The Vial Clamp is a chrome plated hemostat style tool It has a tip shaped to hold the storage vial at an angle of 459 135 when the clamp is closed The clamp can be locked using the hemostat style lock Overall length of the clamp is 195 mm The CryoTong is used to manually transfer a crystal on a magnetic cap from liquid nitrogen to a i magnetic base on a goniometer head positioned in a cryogenic stream and then back to liquid nitrogen The handle is magnetic stainl
6. I I I I I Emergency Stop Button Only press this button in an extreme i emergency such as being locked I I I I search has been completed successfully in a hutch Beamline power will i I I I and a third to indicate that the search has been aborted amp or the search has l be cut AND the storage ring will i taken longer than 45 seconds I dump Key Interlock If these keys are missing then you will be unable to search secure the hutch i I I ere ese A l l Labyrinth Users may feed their OWN cables into the end station through the labyrinth Always ask user support staff for assistance I I PSS Control Panel All PSS functions can be accessed from here Door Unlock Press this button to unlock the door to enter the hutch This will also un secure the hutch I it is ready to be pressed I i NB If you need to secure an area and the light is not flashing check if the i labyrinth keys are in the key interlock and are turned to the lock position i Stack Lamp Legend A quick easy reminder of what the different stack i lamp signals mean Outside the hutch RAPHY BEAMLINE MX2 Search and Secure Process In order to run the beamline the hutches must be secure 1 Enter the end station hutch and check that no one is present 2 Press the flashing search button The alarm will sound and you now have 45 se
7. Po At Rn K K x L2 L2 L2 L2 L2 2 L2 L2 2 2 L 13 13 13 13 13 B LS LL 13 B B B 87 88 89 Fr Ra Ac 58 59 60 61 62 63 64 65 66 67 68 69 70 71 11Ce 11Pr uiNd PmiiSmiiEu 11Gd 11Tb Dy 11Ho Er i 1Tm i1 Yb Lu 2 42 142 12 12 L2 12 12 12 12 142 L L2 12 L3 13 B B bB B ia B B B 90 9 92 uth Paw L2 M1 L2 M1 L3 L3 Select the element for scan from the periodic table and press the Scan button The energy will automatically change to an appropriate value then collection will begin In the Plot tab located above the Periodic Table the heavy elements with absorption edges below the incident energy will show peaks in the spectrum at their characteristic emission energies Excitation Scan of a sample shown to contain Zinc and Selenium The elastic and inelastic peaks are not separated because of the detector resolution and orientation w r t the sample Observe that the K beta peak for Se is relatively small in this sample and it disappears into the tail of the next peak at higher energy Periodic Table Plot Log Excitation Scan of Se K Edge B scan counts cec c cep eX a Tt 10000 20000 Energy eV Kl Inflection eV Peak eV Remote ev Reset ALLOGRAPHY BEAMLINE MX2 L MAD Scan This mode is used to scan the x ray energy against the fluorescence emitted by the sample and subsequently determine the optimal energies for MAD data collection Bef
8. is available after 5pm Currently the following is NOT supported e Manual sample mounting Only automated sample mounting with the SAM robot and Blu Ice interface is available for users on remote access e f a user group or single user is on site but requests remote access assistance from other members of their research team The AS has very strict safety protocols so the person on site will always run the Active Blu Ice interface and the remote access people shall Observe as Passive only At no time should any remote access person s take active control of the beamline when users are in the user cabin and hutch area Beamline staff MUST be informed ahead of time whether this combined user access is to occur so that the appropriate remote access instructions and login permissions can be supplied Page 17 TALLOGRAPHY BEAMLINE MX2 UAL E We re in our labcnats now what E Jw Page 18 ALLOGRAPHY BEAMLINE MX2 5 0 BEAMLINE COMPUTER SYSTEM BLU ICE A dedicated beamline workstation is used for each beamline to control the endstation and store the data and analysis files Log in on these Blu Ice Controls computers using your user name and the password supplied to you at the beginning of your beamtime Remember that Unix is case sensitive Subdirectories are automatically created when starting data collection from the Collect tab If you have brought a portable hard drive to backup your data then the MX
9. pins mount them in an AS cassette and ship them to the AS 4 3 AS CASSETTE KIT If you have scheduled beamtime and specified that you intend to use the robot sample mounting system a cassette kit can be loaned to you Note that at least three weeks advanced notice is required to meet sample loading and shipping turnarounds For additional information about the kit tools including drawings and vendor information please see the SAM hardware web pages at www crystalpositioningsystems com E Cassette Kit A Sample Cassette loaded with 96 Magnetic caps user supplied B Dewar Canister replaces the stock canister in dry shipping dewar C Teflon Ring to support the canister in the shipping dewar D Transfer Handle for handling and transferring cold cassettes E Magnet Tool to mount pins in cassette and to test the size of pins F Guide Tool to aid mounting pins into a cassette with the magnetic tool helps to minimise loop disturbance G Styrofoam Spacer to keep the cassette in place when shipping one cassette B C Not shown Dense foam dewar bath for mounting crystals into the cassette Sample pins The sample cassette is loaded with 96 copper pins All pins must be tested as described in the following pages Note that the AS system supports only Hampton CrystalCap Copper Magnetic pins and the Crystal Positioning Systems pins The only allowed pin size is 18 mm Testing pins with the
10. reads Offline you are not enabled to run Blu Ice on that particular beamline go to the User Tab and type in your password If the GUI is still offline contact the beamline support staff Message Window The message window just above the status bar displays detailed information regarding beamline control operations This area can be enlarged by dragging the upper edge of this window with a mouse For specific information about the experiment see the Log tab Summaries of fluorescence scans are also available from the Scan tab Page 20 ALLOGRAPHY BEAMLINE MX2 5 1 LOG TAB The Log tab can be used to view and save a log of the experiment The log displays the value of the detector and beamstop to sample distance beam size and attenuation energy and the data collection mode It also lists the full path for each file generated during the experiment and the starting phi value for each diffraction image Error messages are also displayed To stop the log tab contents from scrolling during inspection check the pause radio button at the top of the tab Clicking the refresh command button will update the contents of the log Saving and Resetting the Log To save the contents of the log tab to a file click on the download command button This will open a file browser window where you can select the directory and file name to store the log file Trying to write the log to an existing file will result in an error so that you c
11. NE MX2 ANUAL Periodic Table Plot Log Hardware Fp and Fpp from Kramers Kronig transfonm Transform fp Transform fp 49 Transform fpp Transform fpp Fp Electrons A D suoA153 3 dd y N 11700 11800 11900 12000 Energy eV E jy ec von 111872 630 ev Peak 11874 960 ev Remote 12900 000 ev Reset W Link to Run Definition via Update button By clicking the right mouse button on the transform or any other lines in the plot users can change various parameters like line color line thickness symbol shape and color etc Placing the mouse over the plot line will display the x and y coordinates for each point This is useful to find out the f and f values for energies other than the ones written out by autochooch The f and f for the autochooch energies can be obtained from the Log tab or the summary file If you use a different remote wavelength to the one selected by the software you can get the f and f values from tables To zoom in the plot left click on a point of the plot window hold down the mouse key and drag the mouse to define the zoom rectangle The zoom level changes after releasing the mouse button Right clicking on the plot window displays a menu with the option to zoom out Output files The following files are written out after successful completion of a fluorescence scan name scan Contains the raw fluorescence readings name scansmooth exp bip and n
12. ST ru3 1 070 GST ru3 1 071 eo UU an dd E Tm co Mo JN e 122 H E q e M eo e Ww a Ww P e ie w e A n a iu P d og e Ww d Q3 e oo eco co mo GST ru3 1 082 46 00 12410 43 47 00 12410 43 48 00 12410 43 49 00 12410 43 50 00 12410 43 51 00 12410 43 52 00 12410 43 53 00 12410 43 54 00 12410 43 55 00 12410 43 56 00 12410 43 57 00 12410 43 58 00 12410 43 59 00 12410 43 60 00 12410 43 61 00 12410 43 62 00 12410 43 63 00 12410 43 64 00 12410 43 65 00 12410 43 66 00 12410 43 67 00 12410 43 68 00 12410 43 69 00 12410 43 70 00 12410 43 71 00 12410 43 72 00 12410 43 4 73 00 12410 43 74 00 12410 43 75 00 12410 43 76 00 12410 43 77 00 12410 43 78 00 12410 43 79 00 12410 43 80 00 12410 43 81 00 12410 43 82 00 12410 43 83 00 12410 43 84 00 12410 43 85 00 12410 43 86 00 12410 43 87 00 12410 43 88 00 12410 43 89 00 12410 43 90 00 12410 43 the presence of any anomalous scatterers in the sample Scan Mode MAD Scan Excitation Scan e The MAD multiple wavelength anomalous dispersion scan mode is used to selectively target appropriate wavelengths for anomalous dispersion experiments optimized SAD and MAD It allows users to measure the fluorescence counts from a single element when scanning through the energy range in the region of its absorption edge then accurately determine the peak and remote energies most suitable for SAD MAD data collec
13. aintain a full level 8 As you fill the cassette we recommend you record the location of each crystal in a spreadsheet Alternative loading method Transferring pre frozen samples Use Steps 1 through 4 above to prepare the cassette the dewar and tools 5 When ready to load a port place the guide tool on the cassette f and centre on the port To transfer a sample from a vial first tilt the vial and use the red side of the magnetic tool to remove the sample pin g h Be careful to keep the sample under liquid nitrogen at all times Pick up with h nd Maroon side Step 5 f placing the guide on the cassette g picking up the pin and h transferring the pin Page 13 I ALLOGRAPHY BEAMLINE MX2 6 Slide the lower wand slot into the guide tool while keeping the sample under liquid nitrogen Once the wand is in the barrel of the guide tool the wand may be pressed against the back or sides of the guide and pushed downward placing the pin into the port The strong magnet inside the cassette port will now allow the wand to be removed vertically out through the guide tool and the next sample can be Step 6 Using the guide tool transferred 7 Additionally the slotted guide tool may be used for flash cooling samples For flash cooling pick up the sample as described in Step 6 of the previous section and insert the sample through the top of the guide tool Preparing cassettes for shipment Place th
14. align the goniometer for your samples by mounting an empty pin of the same length on the goniometer head and centering it as described in the Blu Ice documentation Verify that you can easily insert the cryo tongs to mount or remove the sample pin without touching the beamstop and other equipment If any crystal has snow flakes it can be cleaned by pouring a small amount of liquid nitrogen over it BUT please carefully cover the sample camera with foil to avoid cracking the lens Also be careful of the beryllium window on the spectrometer Note The Oxford CryojetHT can be used to collect data at temperatures other than 100 K The temperature can be changed using Blu Ice Please speak to your user support staff member for specialised training on how to change the Cryojet temperature Mounting crystals in capillaries Ask the support staff to adjust the Cryojet to accommodate the capillary Staff will supply you with a standard gonio capillary mount EN Page 8 STALLOGRAPHY BEAMLINE MX2 NUAL 4 2 USING THE STANFORD AUTOMATED MOUNTING SAM SYSTEM The SAM system is comprised of a robotic crystal mounter high capacity cassettes stored in a large capacity liquid nitrogen dewar plus an easy to operate graphical interface via the Blu Ice control software The following sections describe how to prepare your crystals for data collection using the AS robotic sample mounting system Follow these instructions to prepare the sample
15. amescansmooth norm bip Intermediate files from autochooch name fp fpp bip Anomalous scattering factors f and f calculated by autochooch Page 35 ALLOGRAPHY BEAMLINE MX2 AL e name summary Summary of the scan including the values for the peak inflection and remote wavelengths and the f and f values for each of them A summary of the scan is also displayed in the Log tab Saving reading and printing fluorescence scans Right clicking the mouse on the plot window opens a menu which allows saving printing and opening fluorescence scan files e The print option will send the current scan plot to the default printer e The open option allows to read in previous scan files The program will open a file browser to help locate the scan files didn t know there were so many ways could make the tech support guy cry e Page 36 STALLOGRAPHY BEAMLINE MX2 UAL 6 0 AROUND THE SYNCHROTRON 6 1 FOOD The synchrotron itself has no cafeteria from which you can purchase food or drink A vending machine with limited snacks is in the User Lounge A e 004 8 amp att a Kad t A lunch van arrives at Ki approximately 11 15am p each day from which hot E fast food sandwiches E Lo EARL eT and a number of other products may be dis le M purchased e g Dr T cigarettes chocolate bars EXE ere a x s and fruit Alternatively Monash University is located directly across the road
16. and has a large food court from which a wide variety of food can be purchased A popular option is Pinewood shopping centre Located in Blackburn Rd a couple of minutes away by car Pinewood contains Subway and many other takeaway food options See map on following pages c etl 2e E e Oxmes Wellington Ra NN Wellington Rd LI o A Ux Tcu P Sa Mtem P 22007 Good mimagery 2007 DigitalGlobe Map da 2008 apData Sciences PSA Ie e Alternatively Turkish food is available from Monash Kebabs Located in Blackburn Rd turn left out of the AS gate and the kebab shop is just over Wellington Road on your left e A comprehensive list of local eateries can be found in the Australian Synchrotron User Resource Manual 6 2 COMPUTER AND ELECTRONIC SUPPLY STORES JayCar Electronics Jaycar 887 889 Springvale Road Near the corner of Dandenong Road 3170 Ph 03 9547 1022 Fax 03 9547 1046 Mon Thu 8 30 6 00 Fri 8 30 8 30 Sat 9 00 5 00 Sun 10 00 4 00 Dick Smith Electronics Springvale Shop 2 819 823 Dandenong Road VIC 3171 Tel 03 9547 0522 Fax 03 9548 5353 Mon Thu 9 00am 5 30pm Fri 9 00am 9 00pm Sat 9 00am 5 00pm Sun 10 00am 4 00pm Rockby Electronics 56 Renver Rd Clayton Ph 03 9562 8559 FOGE Fax 03 9562 8772 Mon Fri 8 30am 4 30pm Sat 9 00am 12 00pm MissionPC Milsisien ze 402 Ferntree Gully Rd your IT profess
17. annot accidentally erase old logs The log file is saved in ASCII format To start a new log file click on the new log button This will clear the log tab contents and start a new log If you do this by accident you may ask the beamline support staff to retrieve the log contents for you 5 2 USER AND STAFF TABS The User Tab lists the user names status and location of all the Blu Ice instances open at the beamline It also displays an authentication window You will need to type in your password if your Blu Ice session has expired the network status in the status bar will be Offline in this case in the practice you will probably only need to do this the first time you open Blu Ice at the beginning of your beamtime Users can not access the Staff Tab staff use this for beamline conditioning and robot inspection 5 3 HUTCH TAB The Hutch Tab allows the users to adjust various parameters for data collection by entering the desired values into the input boxes found in the Hutch Overview menu If changes cannot be made the input box is grayed out or inactive hovering the mouse over the input box will return an error message The changes are shown in red and are not made until the Move button is pressed Hitting the Cancel button restores the edited motor values to their current position Once the Move button is pressed and the changes are initiated the parameter being changed will be highlighted in red Hitting the Abort button wil
18. ase note Ensure that ALL samples shipped to the AS are addressed to Dr Tom Caradoc Davies Otherwise your samples will not be permitted to be imported i e Dr Tom Caradoc Davies Australian Synchrotron MX Beamline Group 800 Blackburn Rd Clayton Melbourne VIC Australia 3168 e A detailed manifest of all your samples including but not limited to source production organism quantity 4 4 REMOTE EXPERIMENTS Complete crystallography experiments can be carried out from remote locations using remote access applications Users wishing to collect data remotely MUST indicate this on their beamtime request form Preparing a remote experiment You will have previously been notified by email of the beamline support staff member whom you have been assigned If you are unsure then it is important that you contact the AS Macrocrystallography group Make sure that your support staff has your contact details during your experiment time preferably a mobile phone Download and install the free NX client software as explained in the remote Unix desktop documentation on the AS Macrocrystallography beamline website Verify that the NX client can be used to successfully access the AS computers before the experiment Page 15 gt TALLOGRAPHY BEAMLINE MX2 NUAL First time remote users should arrange a practice run with their assigned support person before their scheduled beam time Carefully read this User Manual and the most up
19. ating what the robot is doing e You should see your crystal arrive on the screen to the right e Wait for the comment area to say that the robot is back home then you can start to auto centre your crystal via the Hutch tab and then collect your data when the robot is Normal and done Dismounting with the Robot Interface There are two ways to dismount the crystal but you should always first check to make sure the robot indicator is green normal 1 click the dismount button to ask the robot to take the crystal and put it back in the cassette The robot will return to the green norma state once this is finished 11 if you have another crystal in the cassette that you wish to collect simply select this crystal by clicking the new crystal location in the table then click mount The robot will automatically dismount the crystal that is currently on the goniometer take it back to its empty port and then go to the new location to mount the next sample NB this second method will reduce each mount dismount operation by approximately 90 seconds Removing ice off the crystal with the robot The simplest method to remove excessive ice from the crystal is to take it out of the path of the cryojet for a short time This is done by dismounting the crystal and re mounting it again as per the previous instructions Use this feature at your own risk Alternatively this process can be done manually by opening the hutch a
20. ation or not Again if you have already screened your cassette there may be a combination of different colored circles with green meaning that there is a pin in that location black meaning the port is empty or red meaning that there is a port jam in that location select the crystal you wish to mount by clicking once on the circle associated with its cassette location you will need to know this in advance of course It does not matter what the status of the location is It can be either a green known or grey unknown In the uppermost box in this tab it should now describe the cassette position and the crystal location next to the mount button check that the indicator next to the Sample Automatic Mounting mount button shows green normal If middle FS Mount AS it shows yellow busy check the Dmiddig ESI Dismount ae comment just below the indicator to see what the robot is doing You will have to Mem Busy SEEN wait until the robot returns to the green normal done state If it shows red Inspect then you will have to Page 26 Y RA PH Y BEAMLINE MX2 call User Support If everything is ready you can mount your crystal as described below e click the mount button and wait until the robot has gone through the mounting procedure There may be times when it appears that nothing is happening but you should always see the yellow busy indicator and usually a short statement under this indic
21. beamlines have an automated synchronization script that can be set up at the beginning of your beamtime Refer to the laminated instruction sheet at the beamline Data Processing computers Starting Software To start Blu Ice click on the Blu Ice logo on the desktop and login using the login details at the beamline Blu Ice Interface The Blu Ice GUI is organized into tabs Different functions of the software can be accessed by clicking on the tabs Users are allowed to access the following tabs but predominantly the Hutch and Collect tabs are used Hutch A Sample Scan X Collect V Users X Log x l Status Bar The status bar at the bottom of the screen shows the status of the software and beamline hardware The section on the left hand side shows one of three colors depending on the condition of the beamline Green the door is closed and the beamline is ready to run the detector DetectorReady Energy 8180 255 eV Abort User Active Shutter closed 11 46 31 AM is online as in this example Yellow t something inside the hutch is moving or the door is open The message in the window will explain what is happening Collecting Reading Out Detector Energy 12410 434 eV Abort User Active Shutter closed 04 15 15 PM Red there is an error condition that needs action Generally when a user first runs Blu ice they will need to log on to the system using their password in the Users tab If they have not d
22. conds to complete steps 3 amp 4 3 Close the hutch door You will hear it lock The outside secure button will now start flashing 4 Press the secure button outside the end station hutch The indicator will now show orange and the end station hutch is secure If you do not press the next search button in time then the siren will sound the process will be aborted and will need to be restarted from Step 1 If you accidentally unlock the front end optics hutch FEO you will lose beam and will be unable to continue Please contact your user support person DON T enter the FEO PSS Panel Overview Red Beamline is available 4 i 1 Blue Hutch Searched Green Beamline disabled Red Not Searched l l at Control Room Storage Ring HUTCHA sc HUTCH B Y EnSbled Disabled Searched Searched ete On Labyrinth Keys in place c MD Off Labyrinth Keys missing Beamline FE Shutters MATO shutters open gt Enabled LI Opened LI Opened Green Shutter closed Closed bh Closed Shutter control I I buttons press CLOSE CLOSE to activate gt Door locked 2 Door locked Press to _ UNLOCK Red Door Unlock door Locked Security Lock Security Lock Green Door Unlocked 09 29 17 17 08 2007 gy Flashing beam line key out Green Security unlocked beamline inactive Navigation to Red Security Locked Navigation button to Securi
23. d side of the screen tS Starting a Data Collection Run JS Inverse Beam Note that when you create a new run the Wedge nl contents of the old run are automatically copied to dl the new run If you have created few runs and start data collection from a previous run Blu ice will collect frames from the current run and the following runs Note Blu ice will not recollect frames from an already completed run This allows users to collect multiple data sets e g low resolution pass high resolution pass or different wavelengths using different run windows if you click ct immediately editing the run collection will t on the first again In order e After setting all parameters to your desired values ke it continue click the Collect button to collect an image tion at the Yt frame double The network status of your Blu Ice client must be on the image Active to collect an image Further Information on Commands and Parameters Any value that is red indicates that the value for data collection is not the same as the current position If you click on Default the current values of distance axis and energy will be sought and displayed In addition prefix will be set to xtal directory to data username detector mode to normal delta to 1 00 deg time to 1 0 sec and frame start to 001 Click on Update to update the fields for the current motor positions Use the Delete button to delete th
24. e Teflon support ring C inside E the shipping dewar before inserting the La canister B Fill the dewar with liquid nitrogen in the usual manner Using the Transfer Handle D move the cassette into the canister in the dewar minimizing the time the cassette is in the air Remove the transfer handle from the cassette by pushing down on the handle and turning counter clockwise to release it D e 8 0 9 re Two cassettes may be shipped inside one canister However if shipping just one cassette place the styrofoam spacer G on top of the cassette to keep cassette in place during shipment The cassettes are compatible with most dry shipping dewars We recommend using the combination of a MVE model SC4 2V cryogenic shipping dewar with a Taylor Wharton CX100 dewar container We recommend tilt and shock sensors be attached E Page 14 LLOGRAPHY BEAMLINE MX2 M J IP m nm ww PF L 4 3 1 DEWAR SHIPPING How Do I Ship my Dewar to the Australian Synchrotron You will need to fill out a Shipping Form and return it the AS For international shipments the shipping form and AQUIS import permit must be prominently attached to the shipping case The form contains e Exporter contact information the user This includes your name address phone number company name and email These details are required to import goods into Australia e Importer contact information AS International users ple
25. e run that you are in Note that you cannot delete Run O snapshot But be careful when using this command once a run is deleted you cannot return to it and will have to set the parameters again 3 Page 29 ALLOGRAPHY BEAMLINE MX2 Use the Reset button to re use a run But if you do this you should remember to change the image name or destination directory If you do not change the name or destination directory Blu Ice will automatically generate a subdirectory called OVERWRITTEN FILES where old files will be stored This will protect the images from an accidental overwrite Another use of the Reset button is to edit data collection parameters after stopping a started run for instance to change the detector position Data File Naming e Fach data file in your selected run sequence is named in the following way file prefix run number energy number image number img e For example a file could be named data 2 E2 010 img This image is in the 10th frame collected in Run 2 at the 2nd input energy With only one energy level selected the file would be named file prefix run number image number img One Energy Inverse Beam Off Two or more Energies Inverse Beam Off Phi Wedge Phi Wedge Size Size simplest case example example test 1 E1 001 test 1 001 test 1 E1 002 test 1 002 test 1 E1 003 test 1 003 test 1 F2 001 phi 0 3 deg wedge 5 deg 1 energy inverse test 1 F2 002 beam off test 1 F2
26. ess steel i Microscopes Several Leica microscopes are available at the MX i beamlines They have interchangeable lenses and sample lighting One located in the MX2 cabin has digital snapshot capabilities via a local PC User Lounge A lounge has been provided for users to relax or eat It is located on the ground floor near the XFM beamline Tea fresh coffee and Milo i are freely available No food is allowed at the beamline Beverages are permitted but NOT at sample preparation areas E Page 7 DGRAPHY BEAMLINE MX2 4 0 BEAMTIME PREPARATIONS 4 1 MOUNTING SAMPLES MANUALLY When you arrive the hutch door will usually be open If the door is closed do not enter the hutch without first contacting support staff Making room to safely mount samples A user controls computer is available in the user cabin You will be provided with instructions to log in at this terminal and start the Blu Ice GUI see the Blu Ice section of this manual In order to mount samples comfortably the detector should always be moved to about 750 mm and the beam stop to 35 mm Mounting samples in the cryostream When in the cabin the LD4 filling dewar should be used for dispensing liquid nitrogen The LD4 must be re filled outside the cabin using one of the two LD35 dewars and the funnel supplied Gloves and a face shield must be worn by any person within 1 metre proximity during filling Practise before you begin Roughly
27. essarily require you to have uploaded a spreadsheet containing information about your cassettes The only information that is required is the location of your cassettes in the dewar left right or middle Staff will tell you this when they load the dewar This interface can be very useful if you only have a few crystals in a cassette to collect or if you have screened a cassette and have decided which crystals you want to go back to collect data sets The procedure for mounting and dismounting a crystal is e Choose the correct position of your cassette left right or middle by selecting the relevant tab above the pin table E Page 25 YSTALLOGRAPHY BEAMLINE MX2 The interface will probably return a u next to the position indicating that the robot does not know whether a cassette actually exists in that position or not If you have previously screened this cassette then you may see 1 next to the position Either way you may continue Sen a nun oec m Log X Staff V Sample Mounting Robot Control ter an oo men Dismount Sample Annealing Flow Control Stream an wes vfs siwt sae samy mon Eum wee cene pma X Diftrac 31 C1 Dl El F1 G1 H1 11 J1 K1 L1 MH s Bl Ce De me a Ge Bia ls Ji dee dijs 2 You may also see that all the crystal locations in the table show as grey circles This means that the robot does not know whether a pin exists in that loc
28. f time specified by you Only the cold stream is turned off the outer dry nitrogen shroud remains on to protect the crystal from icing To use this type of annealing make sure the Flow Control tab is selected select the annealing time using the anneal time pull down menu as shown above then choose the length of time you wish the cold stream to be off the maximum time is 10 seconds but typically a time of between 2 5 seconds is all that is required To start the annealing process press the Start Sample Annealing button The button will initially turn red as shown below and you will see the warning Confirm may destroy sample To activate annealing you need to click this button a second time within 2 seconds otherwise the button reverts back to the grey Start Sample Annealing button This is to prevent accidentally hitting the button Use this feature at your own risk E Page 28 TALLOGRAPHY BEAMLINE MX2 5 5 COLLECT TAB Run calectng ln elete ese 1 Collecting a Snapshot Prefix GST ru3 Directory data marccd frames bm 1 ul Run tab 0 is dedicated for taking snapshots in order g p Detector wma yj to test crystals and plan strategies for data collection All other Run tabs can be used for collecting a data ae RE er se t Attenuation 0 000 Axis Phi Delta 1 00 deg Time 5900 s e To create a new run click on the tab below the ERE O tab on the far right han
29. he same way as on site See section 5 The beamline can be monitored using the standard video feeds in Blu Ice or by using the web based beamline video system What do I do when I finish When you finish your experiment contact the beamline support staff use e mail between 11pm and 7am Once staff have been notified they will put your cassette s back into the shipping dewar as soon as they are on site then attach the return form supplied by you and arrange for its shipment _ Page 16 SRYSTALLOGRAPHY BEAMLINE MX2 Note that your dewar cannot be shipped unless you provide a return shipping form Users will need to supply ALL documentation required to return ship dewars and or samples including an air bill If you wish to store your dewar at AS between experiments you do not have to provide a return shipping form Instead inform your user support person It is important that you also notify the support person for your next experiment Fill out the end of experiment survey form Feedback is essential to help us improve your user experience The more information you provide in this survey the better the service we can provide http survey synchrotron org au 4 5 REMOTE EXPERIMENT SUPPORT For questions or problems that develop during the experiment please consult the documentation before contacting support staff You will be assigned a support person whom you can ring 24 hours a day Reduced support
30. ionals http www missionpc com au Ph 1300 853 889 Mon Fri 8 30am 4 30pm Sat 9 00am 12 00pm E Page 38 RYSTALLOGRAPHY BEAMLINE MX2 CPL Computers and Parts Land 7 Howleys Rd Nottinghill LI CPL www cpl net au Phone 03 8542 8688 my Fax 03 9562 8781 COMPUTERS AND PARTS LAND Email cplnott cpl net au This store has a very comprehensive inventory of computers and computer parts at very reasonable prices 7 0 MAP OF FACILITY Biochemistry A 7 Laboratory y BW y Control Room y e mezzanine L e V MX Beamlines o AE jm z a a Q User 4 Lounge o a Z f First Aid i E LT Toilets se MX Offices Pia o M 45 Ea e on mezzanine OE Reception E Page 39 LLOGRAPHY BEAMLINE MX2 d Dg bm 2
31. l stop the changes while they are being made In general all motors will remain at the position at which the Abort button was pressed Page 21 STALLOGRAPHY BEAMLINE MX2 NUAL Hutch V Sample Y Scan X Collect X Users tog X Staff V mem T mmn De Sample Lights Control E not available on this beamline P iili 5 ii dii 3 8 A Ss E Detector Reay Energy 8180 255 eV Abort User Active Shutter closed 11 46 31 AM Pull Down Menus e The pull down menus next to input boxes show the minimum and maximum values for the particular control with a range of values in between Distance 72 000 mm 72 0005 650 0000 e Any values can be input within this range ia een eS Entering values outside the range is strongly f ux m onc BB discouraged you may get an error message E j franc om or hit a motor hardware limit which will result in miscalibration of the motor This is particularly detrimental in the Energy change pull down menu gn i e Clicking on the units will produce another drop down menu with alternative units e Clicking on the name of the parameter will produce a window presenting the option to undo the last change of that parameter If your experiment requires data collection outside the range provided contact your support staff Manually mounting the crystal e In the Blu Ice Hutch tab move the detector and beamsto
32. lly or horizontally by one pixel Sample Orientation The Omega and Kappa motors are currently locked to avoid collisions with the detector and other beamline hardware If Omega or Kappa values need to be changed please contact your support staff Adjusting Beam Attenuation When the detector is saturated or has too many overloads the beam needs to be attenuated to ensure accurate data collection Attenuating the beam can also account for exposure times shorter than the m Attenuation rotation time of phi Use the drop 00 v down menu or type a percentage to attenuate by Aluminum filters are used to attenuate the beam lon Chamber 8959 counts High energy beams cannot be fully attenuated by the aluminum filters Raising the energy of the beam will lower the attenuation Beam Size e If this function is available during your experiment click on the windows labeled Width j Beam Width Beam Height and Height under the beam size label The 4000 v mm x 4 000 v mm white box on the Hutch monitor gets updated automatically to the input value Like all other Blu Ice parameters the color of this box becomes red if the current value is not same as the value in the input box Clicking on the units will open a drop down menu that allows the units to be changed Ideally the beam size should be the same as the crystal size However due to horizontal crossfire beam sizes of less than 100 mic
33. magnet tool Page 9 ALLOGRAPHY BEAMLINE MX2 UAL Hampton mounted Hampton Mounted Cryoloop in a Micralube cryo loops should be cut at the Break Here Largest CryoLoop shown segment closest to the loop for o use with the CrystalCap Copper pins 1 5 A A ti B Left Preferred size of pin Do not exceed the maximum MicroTube length shown in the diagram mE Or excess cryo All pins must be tested to ensure they fall within the ctant on the pin allowed tolerances we have discovered some 3 i t use pins with irregular pins that if used would have damaged the epoxy glue on AS sample mounting system To test your pins place es at post It them on the end of the magnet tool on the red mark Pass Fail Red line is ail varnish and showing m e effect Only use pins that completely cover the red mark without forcing down Pins that fail this test should not be used Using The Slotted Guide Tool It is important to keep pre frozen samples at liquid nitrogen temperatures during their transfer into a different storage container Therefore a slotted guide tool has been developed as an aid to safely guide sample pins into cassette ports while allowing the sample to remain under liquid nitrogen during this transfer Page 10 TALLOGRAPHY BEAMLINE MX2 Used to remove pins Red side used for from cassette testing pins and to contains a stronger insert pins into magnet cassette
34. nd placing a business card or similar in the path of the Cryojet for a very brief moment however this must be done with care not to disturb the beamstop and surrounding apparatus Sample Annealing It is known that protein crystals have an underlying granular or mosaic structure giving rise to blocks of well ordered crystalline lattice which i Page 27 TALLOGRAPHY BEAMLINE MX2 produce sharp diffraction peaks surrounded by disrupted water rich regions which produce either diffuse scatter or no diffraction at all The size of these blocks becomes smaller when the crystal is put under stress associated with flash freezing predominantly due to the expansion of the bulk solvent in the solvent channels and this increase in microheterogeneity of the mosaic blocks leads to an increase in crystal mosaicity and a reduction in resolution and diffraction intensities Crystal annealing where the temperature of the frozen crystal is either raised to just above the freezing point of the cryoprotectant or by several degrees but without thawing is a method which has been used successfully to improve the diffraction quality of flash cooled crystals Flow Control Stream Block anneal time 0 000 s Start Sample Annealing Abort Sample Annealing Sample Annealing Flow Control Stream Block Flow Control Annealing In Flow Control annealing the cold stream can be temporarily stopped for a certain length o
35. ng and examining the Fluorescence Scan The program autochooch automatically calculates the anomalous scattering factors from the fluorescence data The f and f plots are displayed in the Plot tab as well as the suggested peak maximum f inflection minimum f and remote high f and f energies for MAD data collection Periodic Table 1 Plot Log Hardware 1 Fp and Fpp from Kramers Kronig transfonm A ntm a gt a s a 4 11700 11800 11900 12000 Energy eV Kl T scan fluor smooth smooth Fluorescence 0 02 imeetens M1637 710 eV Peak 12092 770 eV Remote 12900 000 eV Reset W Link to Run Definition via Update button e The selected energy values can be adjusted by moving the vertical cursors The cursors can be moved by clicking on them with the middle mouse button Right clicking on the cursors will give options to change the cursor color cursor thickness and to delete the cursor This will update the energy values selected for data collection e Checking The Link to Run Definition via Update box allows exporting the energy values into the collect tab this is the default after a successful scan Pressing the Update button in the Collect Tab will then import the energies for MAD data collection e You can display the raw fluorescence counts by clicking the right mouse button on either side of the plot and selecting a new Y axis label E Page 34 RYSTALLOGRAPHY BEAMLI
36. ns are Sm or Eu Consult the support staff for help with selecting the edge e The directory and prefix determine the location and Se Pee name of the scan output files The update button will set errores M the directory to data yourid and prefix to test If you used the screening tab to mount the crystal the update r Scan Parameters button will set the directory and prefix to the directory Update and crystal name used in the screening tab m The Start button will start the scan operation po ii Edge Se K Before starting scanning the energy the software will automatically attenuate the beam to avoid saturating the fluorescence detector Several beam filter Energy 12658 000 ev Time 1 000 s combinations are tested You can monitor this from the hardware tab or in the electronics rack filter control panel e Stop will interrupt the scan and move all the motor positions to their initial values Abort will stop all motors immediately but the beam filters will be returned to their original configuration E Page 33 TALLOGRAPHY BEAMLINE MX2 NUAL e Click on the Plot tab next to the Periodic Table tab to display the plot of the spectrum e The Log tab displays the fluorescence readings during the scan If the initial scan looks noisy large oscillations in the fluorescence counts from points to point comparable to the edge height the scan time can be increased to improve the signal Analyzi
37. on the side of the dewar Then push the cassette forward a until the bottom of the cassette is touching the far wall of the dewar and does not roll or slip The guide tool should be pre cooled on the side dewar shelf b To prevent condensation on the metal portions of the guide it may be stored on b storing the guide tool the shelf between loading samples Pre Cool Guide Tool On Small Shelf Area Step 3 a placing the cassette in the dewar 4 Using the transfer handle rotate the sample cassette so that the row with the desired cassette port is facing upward 5 When ready to load a port place the guide tool on the cassette c and centre on the port Put a pin onto the red side of the magnet tool d and pick a crystal e from your tray 6 Flash freeze the crystal by placing the pin down through the Step 5 c Placing the guide tool on the cassette d handle of guide tool and Putting the pin on magnet tool and e picking the crystal into the cassette port making sure you minimize the time the crystal is in the air E l Page 12 TALLOGRAPHY BEAMLINE MX2 Step 6 Flash freezing the crystal 7 Use the lid to cover the dewar when you are not mounting crystals as this prevents ice from accumulating in the liquid nitrogen and getting into the cassette ports The cassette should not be stored in the loading dewar for more than 20 minutes and liquid nitrogen should be topped up frequently to m
38. one so then the message logged out will appear logged Out gt Energy 12657 973 eV Abort User Shutter closed 12 04 25 PM Page 19 gt TALLOGRAPHY BEAMLINE MX2 NUAL The Energy indicator displays the current energy of the beamline and by clicking on the units next to the reading allows you to change from eV to angstroms or keV Energy 12657 973 ev Abort User Shutter closed 12 04 25 PM Once the user has logged on they can become the active user by clicking the Passive button This button will then show Active in red Only one user at a time may be active which prevents multiple users trying to move motors at the same time User Active Shutter closed If you find at any point during your data collection that the beamline no longer allows you to change parameters or type file names in the Collect tab you should first check that you are still the Active user The final indicator on the status bar tells you whether the shutter is open or closed and will display this ite users please during normal data collection or screening By clicking am on the button itself you can toggle between open and upport VFAT or closed but this is of little use during normal data T3 file systems collection and has the potential to destroy crystals Y external ire hard drives Suggested that ring a minimum OGB per 24 hour without collecting data Network status If the status
39. ore this is done users should run an Excitation Scan to verify that the relevant element is actually present in the sample Selecting an X ray Absorption Edge The desired absorption edge can be selected from the Periodic Table tab Scan Mode Periodic Table Plot Log 1 Hardware nob cd od 2 Select an X ray Absorption Edge A w Excitation Scan Select an edge by i ge Edge Se K B e UN o wal Ne 1 1 Scan sample to determine cl icki ng on a peak inflection and remote u E Energy 12658 000 eV 13 14 15 16 17 18 ti d K energies for MAD Na Mg Al Si P S Cl Ar articular edge e L2 L3 g d d mK ca Sc T my mcr Mn Fe Co Ni cu Zn E Ga Ge mAs A Se Br Kr a n Scan Parameters K K K K K K K K K K K K K K Update press the Scan WRb Sr Y zr uNbrMo Te riRuriRh riPd Ag ri Cd Lin tiSniiSb iTe rl xe Prefix test K K K K K K K K K K K K K K K K K butto n Directory idatafbictl tiCs LiBa ila EL Ta HW Re Hos L Bt Au Hg n Pb Bi Pol At Rn Edge Se K K KIRK ji B ds 3 3 ls ls is ls ls 97 899 89 Energy 12658 000 eV Fr Ra Ac H H it Te 1 000 S8 59 60 61 82 63 64 65 66 67 68 69 70 7 L1 Hf L1 Ta L1 Wy j iiCe iiPr aNd PmiiSmiiEu 11Gd 11Tb 11Dy 11Ho 11Er LiTm 1Yb 11Lu L2 i l2 D bp wp EN u BEEER eee ee 90 9 9 Sto T P U L3 L3 H3 mcan gm egin Or L3 L3 For some elements you can select different edges L1 L2 L3 As a rule of thumb always select L3 for heavy elements exceptio
40. p away from the goniometer for easy mounting typical safe distances are detector 750mm beamstop 35mm or Page 22 LLOGRAPHY BEAMLINE MX2 ld Practice mounting a pin with a blank loop onto the goniometer to make sure your system is compatible with our cryo stream Contact staff if you run in to any problems e Check that the cryo stream is aligned correctly nozzle to sample distance should be 10mm e Mount your sample on the goniometer head taking care NOT to hit the beamstop e Move the beamstop back into place using Blu Ice e Use the resolution predictor to calculate the optimal beamstop and detector distances If you will be using the Stanford Automated Mounting SAM robot for mounting your crystals see the Sample tab and refer to Section 5 4 for further instructions Crystal Centering 1 Select the Sample tab on the video display Select Zoom Level 2 Click on the sample to center it Low Med High 3 Rotate phi either or 90 degrees Move Sample ail 4 Click on the sample once again to center gt de Repeat steps 2 to 4 to align the crystal accurately pe If you want to hit the crystal in a very precise spot and Rotate Phi you cannot click on it accurately enough with the mouse 90 90 180 you can use the Move Sample buttons The double arrow buttons translate the sample horizontally by half a Center Loop screen The single arrow buttons translate the sample vertica
41. ron width will reduce the beam intensity Energy e To change the energy use the box labeled Energy ETE 7 uu 6740967 ev e BE CAREFUL when it is first started Blu Ice shows the energy in eV The energy units can be changed to keV keV and by clicking on the current unit Click Start to A initiate any changes that you make e The input value units must be the same as the selected unit Entering a value of a different unit will result in an error Adjusting Detector Position To adjust the detector distance or angle change the values in the corresponding box You will notice in the Resolution Predictor that the predicted resolution circles move See Determining Resolution Limits for more details Pressing Move will move the detector to the set position To view the detector position on video go to the Hutch Tab in the video section and select overview from the presets on the left Resolution Predictor Determining Resolution Limits p lt e The high and low resolution limit at a particular detector and beamstop position may be determined using the box labeled Resolution Predictor When a change is made in the detector position beamstop y position or energy the view in this box is updated b d automatically e The label on the largest circle that fits in the detector shows the resolution to which complete data can be collected Partial circles limit resolution shells that will be incomplete
42. s Wand and slotted guide tool The slotted guide tool consists of 1 a long magnetic wand with two slots in the middle and 2 a loading guide with a track on the handle that accommodates the slots on the wand tool Use the slot closest to the red or Use 1 slot maroon side of wand weak magnet for loading samples When unloading Samples the wand is turned around and the opposite slot and stronger magnet is used It is recommended for use with the custom foam storage dewar The circular cutout in this dewar may be used to hold samples in cryo vials during transfer Using the slotted guide tool Loading the sample cassette with crystals 1 Attach the transfer handle to the empty sample cassette it has a spring loaded bayonet fitting Firstly place the locking pins into the slots at the top of the cassette then push down the handle and rotate clockwise until the handle locks in place Leave the cassette on the transfer handle 2 The custom foam dewar should be filled up to the internal indicator ledge This takes about 4L of liquid nitrogen Step 1 Attaching the transfer handle Note that it will be necessary to top up to the cassette the liquid nitrogen level after inserting a warm cassette or tools E Page 11 OGRAPHY BEAMLINE MX2 Step 2 Filling the dewar 3 Once the dewar is filled and equilibrated place the cassette in the dewar and tilt the transfer handle until it rests inside the notch
43. tion based on that specific sample Excitation Scan Mode The Excitation Scan mode measures and charts the fluorescence counts from all elements present in the sample if they have an absorption edge below the chosen excitation energy Excitation scans are very useful for the identification of heavy elements in a crystal They take less time than the MAD scans and thus are a faster way to determine the presence of a heavy atom derivative ligand in the sample Page 31 Tals ScanMode wv MAD Scan Excitation Scan Use multi channel analyzer to perform a fluorescence scan at a particular energy The recommended energy is 500 0 eV above the edge energy r Scan Parameters Update Prefix test Directory data blcl Edge Se K Energy 13158 000 eV Time 10 000 s Periodic Table Plot Log Hardware H Select an X ray Absorption Edge u i Be Edge SeK Ma c y Po PE Ne ua ave Energy 12658 000 eV 3 45 Bp Bo Ho 19 2 21 m 23 25 26 0027 2 2 30 31 32 33 34 035 36 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr K K K K K K K K K K K K K K 24 37 38 39 40 A 42 43 44 45 46 47 48 49 50 51 52 53 54 uRbuSr nY Zr 11Nb11Mo Te iiRu Rh Pd 114g ii Cd iiln 11Sn 11Sb aTe 111 11Xe K K K K K K K K K K K K K K K K K 55 56 57 372 73 74 75 6 7 39 79 81 82 83 84 85 86 11 s Baila LiHf aTa 114 Li Re 110s iile Pt wAuLiHgiill 1 Pbi1Bi
44. to date details on the MX website PLEASE only use sample pins that are compatible with the AS robot Beamline staff reserve the right to remove incompatible pins from any users cassettes to avoid potential damage to the endstation and robot Dewars should arrive at AS at least two days in advance of beam time Use the Shipping Dewars to AS form The tracking number must be included in the form Also make sure that you specify that you are doing a remote experiment by clicking the corresponding check box and filling in the requested information for return of the dewar Remote data collection Remote experiments are scheduled to start at the nominated time on the User Office correspondence However support staff may contact you to start earlier in the day Support staff will mount your cassette s search and lock the experimental hutch probe cassettes for jammed pins and enable access to Blu Ice Support staff will then contact you and inform you of the following e Cassette locations left middle or right position in the robot dewar you can then assign the excel spreadsheet s to the correct location in the dewar from the Blu Ice Sample tab refer to Section 5 4 e Pin locations that might cause a port jam when a real port jam is detected during the probing the corresponding cassette port is automatically disabled When can you start your experiment Data collection and data processing are carried out in exactly t
45. ty Pages System page not used 2 0 CHEMICAL BIOLOGICAL AND CRYOGENIC SAFETY i Occupational Health and Safety Users will need to complete facility specific safety training The training information will be provided in advance User Office website and the test should be approximately 30 minutes This will need to be completed the day before your experiment is due to commence If this safety training is not completed users will i not be allowed to work unescorted beyond normal staff hours 8am 5pm On completion you will be issued a photo ID badge which will need to be displayed at al times Cryogenic Safety Blue cryogenic safety gloves and face shields are provided for your I protection when decanting liquid nitrogen into a dewar Standard i Operating Procedures SOPs can be found attached to each liquid i nitrogen dewar i In the experiment hutch cotton gloves covered by nitrile gloves and safety glasses are required to handle liquid nitrogen Users are expected to provide their own cotton gloves as there is no regular laundry service at the AS I Chemical Safety i Water Isopropanol Ethanol and Acetone are provided in I small quantities Nitrile gloves and safety glasses are required to handle any chemical Users should supply a i Material Safety Data Sheet for any chemical they bring into _ the facility Users are responsible for the safe disposal of their own chemicals The
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