Changes for page CFEL TapeDrive: Serial Crystallography

Last modified by chatzies on 2025-11-27 11:35

From 17.1 to 18.1 From 43.1 to 44.1

From version 18.1

edited by ahenkel
on 2021-12-02 14:20

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To version 43.1

edited by ahenkel
on 2021-12-12 23:49

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@@ -1,7 +1,16 @@
--[[image:attach:TapeDrive_beschriftet.PNG||height="400"]][[image:attach:TapeDrive scheme.png||height="400"]]
++{{layout}}
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
--**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)**
++\\
++\\
++
++\\
++
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
++
  * remove vortex
  * beamstop to out-position?
  * remove goniometer. The airbearing should be stopped (p11/servermotor/eh.1.01)
@@ -50,7 +50,7 @@
  \\
--**14.2 Sample characteristics and preparation**
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 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.
@@ -62,41 +62,54 @@
  \\
--**14.3 Connecting sample to ElveFlow, sample exchange
--**
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
++** ===
--[[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]][[image:attach:20211201_095205.jpg||height="250"]][[image:attach:20211201_095232.jpg||height="250"]]
++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"]]
++
  \\
--**14.4 TapeDrive operation
--**
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
++** ===
--The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open, shortly after a small window.
++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"]]
--* **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"]]
++**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"]]
--* **Sample nozzle:**
--** Click an the 'nozzle' icon.
--** (((
--The nozzle position can be adjusted in xyz by clicking on the arrows up and down. Step size can be varied, 1mm steps are rather big and should be used carefully, for y-movement always use a stepsize <= 0.5mm.
++==== {{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.
--\\Adjust the nozzle position visually 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 X-ray beam (red X) and write down the absolut nozzle position. From there move the nozzle in +x to your desired distance.
--(% class="wrapped" %)
++
++(% 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.
++
  |=(((
  \\
  )))|=(((
@@ -137,15 +137,23 @@
  be careful with -z, tape could be pushed out of focus
  )))
--(% 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);" %)** !!!**(%%)**
++**
  \\**
  )))
--** [[image:attach:kamzik_nozzle.PNG||height="400"]]
++* [[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:
@@ -158,16 +158,235 @@
  \\
--**14.5 Tape roll exchange**
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
--**[[image:attach:20211201_094111.jpg||height="250"]][[image:attach:20211201_094101.jpg||height="250"]]**
++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"]]
++**
++
  \\
  \\
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 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="single"}}
++{{layout-cell}}
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 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//
++
  \\
++Click "Start" icon in kamzik.
++
++[[image:attach:kamzik_run-tile.jpg||height="400"]]
++
++----
++{{/layout-cell}}
++{{/layout-section}}
++
++{{layout-section ac:type="two_equal"}}
++{{layout-cell}}
++**Check list:**
++
++(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
++
++* Open BS1  (//CrystalControl)//
++* Put collimator in (//CrystalControl)//
++* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
++* Open fast shutter (//CrystalControl)//
++* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
++* Close fast shutter (//CrystalControl)//
++
  \\
++**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//
++
  \\
++
++(% style="color: rgb(153,51,102);" %)**//Current bug~://**
++
++(% style="color: rgb(0,0,0);" %)You need to "Stop" run in kamzik manually after all images have been acquired. This moves the shield up and closes the fast shutter. Afterwards you can start a new run by clicking "<Call>".
++
++
++(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
++
++(% class="code" %)
++(((
++      cd /gpfs/current/raw/scan_frames
++      watch "ls -lrt <run number>/ | tail"
++\\\\\\\\
++)))
++{{/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-14.9Troubleshooting"/}}14.9 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
++)))
++{{/layout-cell}}
++{{/layout-section}}
++{{/layout}}

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@@ -1,1 +1,1 @@
--235039093
++236824590

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@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/235039093/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/236824590/14. Serial Crystallography: CFEL TapeDrive

Changes for page CFEL TapeDrive: Serial Crystallography

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