Changes for page CFEL TapeDrive: Serial Crystallography

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edited by ahenkel
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edited by ahenkel
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Title

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--Serial Crystallography: CFEL TapeDrive
++14. Serial Crystallography: CFEL TapeDrive

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++{{layout}}
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
++
++\\
++
++{{toc minLevel="2"/}}
++
++\\
++
++----
++
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
++
++suspension of microcrystals, **at least** 200 µL with 20% crystal density(more is always better), size range: 2-30 µm, **tip:** bring some mother liquor for washing, filtering, diluting etc.
++
++Preparation:
++
++* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
++
++[[image:attach:20211201_095534.jpg||height="250"]]
++
++\\
++
++----
++
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
++** ==
++
++After filtration, screw the ElveFlow connector to your Eppendorf or Falcon tube. Make sure that the yellow-ish line goes to the bottom of your tube. You can adjust the length by unscrewing the blue fitting on top and pushing/pulling the yellow-ish line. **Don't forget to tigthen the blue fitting afterwards!**
++
++Be aware to which channel and nozzle line your sample is connected.
++
++            Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
++
++            Green → Channel 2, substrate line (nozzle capillary is marked in black)
++
++[[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
++
++After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
++
++[[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
++
++\\
++
++----
++
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
++** ==
++
++The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
++Now start the client. Same thing, a terminal will open, shortly after a small window.
++
++Click 'Devices' in the **client session** to open the control window.
++[[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
++
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
++
++* Click on the 'main tape' icon
++* Change the velocity by typing anything from **0.3-3.0 mm/s**
++* Common velocity is 1.0-1.5 mm/s
++* kamzik displays the used tape in m and %. At 98% the tape will automatically stop since the rolls need to be exchanged at this point.
++\\
++* [[image:attach:kamzik_tape.PNG||height="400"]]
++
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
++
++* Click an the 'nozzle' icon.
++* (((
++The nozzle position can be adjusted in xyz by clicking on the arrows up and down. (Double arrow = 10 steps). Step size can be varied, 1mm steps are rather big and should be used carefully.
++The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
++
++
++(% style="color: rgb(255,0,0);" %)**!!! **(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color: rgb(255,0,0);" %)** !!!**(%%)
++\\Adjust the nozzle position by eye until it nearly touches the tape and roughly meets the X-ray interaction point. Then, move to the control hutch to use the on-axis microscope for fine adjustment. Move the nozzle tip to the beam position (red X) and write down the absolut nozzle position. From there move the nozzle in +x to your desired distance.Different distances combined with the tape speed result in several delay times for time-resolved experiments.
++
++(% class="wrapped" %)
++|=(((
++\\
++)))|=(((
++direction
++)))|=(((
++recommended step size
++for visual adjustment
++)))|=(% colspan="1" %)(((
++recommended step size
++during data collection
++)))
++|(((
+++x
++)))|(((
++away from X-ray interaction point
++)))|(((
++1.0 - 0.5 mm
++)))|(% colspan="1" %)(((
++0.1 - 0.2 mm
++)))
++|(((
+++y
++)))|(((
++up
++)))|(((
++1.0 - 0.5 mm
++)))|(% colspan="1" %)(((
++0.1 - 0.2 mm
++)))
++|(((
+++z
++)))|(((
++towards detector tower, away from tape
++)))|(((
++0.5 - 0.2 mm
++)))|(% colspan="1" %)(((
++0.1 - 0.2 mm
++be careful with -z, tape could be pushed out of focus
++)))
++
++**
++\\**
++)))
++* [[image:attach:kamzik_nozzle.PNG||height="400"]]
++
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
++
++* The chiller circulates fluid through the gas nozzle.
++
++\\
++
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
++
++\\
++
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
++
++\\
++
++Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
++
++                                        xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
++                                        password: //written on control laptop (changes every 6 months)
++//
++
++\\
++
++\\
++
++----
++
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
++
++The tape stops automatically at 98% used length, if you need to change the rolls for orther reasons, stop the tape (velocity = 0.0 mm/s).
++
++* Remove the (almost) empty feeder roll by pulling it upwards.
++* Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
++* Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
++* Cut the first cm of the new tape roll, directly behind the black sticky part.
++* Place new roll on roll holder and use sticky tape to attach the end of the old tape to the beginning of the new roll.
++* Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
++* Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
++* Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
++* Attach new tape to the empty roll by using some sticky tape.
++* Close tape stabilizer.
++* Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
++
++**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
++**
++
++\\
++
++\\
++
++**
++**
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++----
++
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
++
++start chopper gui from terminal:
++
++(% class="code" %)
++(((
++            cd /gpfs/local/shared/ChopperControl
++)))
++
++(% class="code" %)
++(((
++            python chopperControl.py
++\\\\
++)))
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="two_equal"}}
++{{layout-cell}}
++                     [[image:attach:20211212_233140.jpg||height="250"]]
++{{/layout-cell}}
++
++{{layout-cell}}
++**Chopper → no Chopper**
++
++* decrease frequency by max. 10 Hz steps\\
++** click arrow down 10x, "Set", arrow down 10x, "Set", ....
++* at frequency = 10 Hz, click "Stop"
++* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
++
++(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
++
++* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
++* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
++** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
++* (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="two_equal"}}
++{{layout-cell}}
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
++
++Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
++
++(% class="code" %)
++(((
++                      xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
++                      password: written on control laptop (changes every 6 months)
++)))
++
++                               //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
++
++\\
++
++**Check list:**
++
++(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
++
++(% style="color: rgb(0,0,0);" %)Click "Safety" icon in kamzik.
++
++* Put collimator in
++** Click "<Call>" next to //collimator_in//
++
++\\
++
++* Open beam shutter BS1 in //CrystalControl//
++{{/layout-cell}}
++
++{{layout-cell}}
++[[image:attach:kamzik_safety.PNG||height="400"]]
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++----
++
++Click "Start/Run" icon in kamzik.
++
++[[image:attach:kamzik_run-tile.jpg||height="400"]]
++
++----
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="two_equal"}}
++{{layout-cell}}
++**Set run parameters and go 🏃💥**
++
++1. Set your desired No. of frames
++1. Match exposure time with chopper setting
++1. Check trigger setting and match to chopper setting
++1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
++1. To start the run, click "<Call>" next to //exposure time//
++
++\\
++
++\\
++
++**After data collection/before entering the exp. hutch**
++
++1. Go to "Safety" in kamzik.
++1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
++11. Drive the collimator out
++11. Drive the detector back to 1500 mm
++1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
++
++[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
++{{/layout-cell}}
++
++{{layout-cell}}
++(% class="wrapped relative-table" style="width: 100.0%;" %)
++|=(((
++Parameter
++)))|=(((
++explanation
++)))|=(% colspan="1" %)(((
++value
++)))
++|(((
++Images number
++)))|(((
++Set number of frames you want to collect
++)))|(% colspan="1" %)(((
++usually 100k - 200k, but adjust according to hitrate
++
++orientation: 10 % hitrate needs at least 100k images
++)))
++|(((
++exposure
++)))|(((
++exposure time of Eiger
++
++\\
++)))|(% colspan="1" %)(((
++chopper at 133 Hz → 3.7 ms
++
++chopper at 66 Hz   → 7.7 ms
++
++no chopper            → 7.7 ms
++
++----
++)))
++|(((
++run id
++)))|(((
++changes automatically
++)))|(% colspan="1" %)(((
++\\
++)))
++|(% colspan="1" %)(((
++Detector distance
++)))|(% colspan="1" %)(((
++current detector postion readout
++)))|(% colspan="1" %)(((
++\\
++)))
++|(% colspan="1" %)(((
++move_detector (distance)
++)))|(% colspan="1" %)(((
++Set detector distance
++)))|(% colspan="1" %)(((
++200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
++)))
++|(% colspan="1" %)(((
++Diode voltage
++)))|(% colspan="1" %)(((
++read out of diode
++)))|(% colspan="1" %)(((
++**~~ 0   !!! higher values indicate missaligned beam stop!!!
++Call local contact
++**
++)))
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++----
++
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
++
++* (((
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
++
++* Tape roll empty?
++* motor connected (icon green)?
++)))
++
++\\
++
++* (((
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
++
++* displayed in green=connected?
++* nozzle holder colliding somewhere?
++* motor limits reached? → position displayed in red
++)))
++
++\\
++
++* (((
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
++
++* channel turned on?
++* Sample empty?
++* Nozzle or lines clogged? → flush with water, change nozzle
++)))
++
++\\
++
++* (((
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
++
++* First, restart kamzik (server+client) and see if this solves the issue
++* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
++* (((
++If nothing works, kill the Simplon process and then start the server again:* (((
++(% class="code" %)
++(((
++ssh haspp11exp03
++)))
++)))
++* (((
++(% class="code" %)
++(((
++ps -ef | grep Simplon
++)))
++)))
++* (((
++(% class="code" %)
++(((
++kill -9 simplon_process_id
++)))
++)))
++)))
++)))
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++\\
++{{/layout-cell}}
++{{/layout-section}}
++{{/layout}}

Confluence.Code.ConfluencePageClass[0]

Id

@@ -1,1 +1,1 @@
--235031814
++250178623

Title

@@ -1,1 +1,1 @@
--Serial Crystallography: CFEL TapeDrive
++14. Serial Crystallography: CFEL TapeDrive

URL

@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/235031814/Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/250178623/14. Serial Crystallography: CFEL TapeDrive

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