Changes for page CFEL TapeDrive: Serial Crystallography

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

From 19.1 to 18.1 From 41.1 to 40.1

From version 40.1

edited by ahenkel
on 2021-12-12 23:16

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To version 19.1

edited by ahenkel
on 2021-12-03 09:50

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@@ -1,20 +1,7 @@
--{{layout}}
--{{layout-section ac:type="single"}}
--{{layout-cell}}
++[[image:attach:TapeDrive_beschriftet.PNG||height="400"]][[image:attach:TapeDrive scheme.png||height="400"]]
++**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)**
--{{toc/}}
--
--[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
--
--\\
--
--\\
--
--\\
--
--=== {{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)
@@ -63,7 +63,7 @@
  \\
--=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 Sample characteristics and preparation** ===
++**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.
@@ -75,27 +75,17 @@
  \\
--=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
--** ===
++**14.3 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!**
++[[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]][[image:attach:20211201_095205.jpg||height="250"]][[image:attach:20211201_095232.jpg||height="250"]]
--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-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
--** ===
++**14.4 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.
@@ -103,26 +103,24 @@
  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**
++* **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"]]
--* 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.
--* (((
++* **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.
--
--(% 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" %)
  |=(((
  \\
@@ -167,20 +167,12 @@
  **
  \\**
  )))
--* [[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:
@@ -193,23 +193,17 @@
  \\
--=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
++**14.5 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!**
++* Cut the tape with some cm overlap to glue to the new 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".
++* Cut the first cm of the new tape roll, directly before the black sticky part.
++* Use this sticky part to attach the end of the old
--**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
++**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]]
  **
  \\
@@ -216,150 +216,8 @@
  \\
--=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
--
  \\
--=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Datacollection"/}}**14.7 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-14.8Troubleshooting"/}}14.8 Troubleshooting ===
--
--* (((
--==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
--)))
--* (((
--==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
--)))
--* (((
--==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
--)))
--{{/layout-cell}}
--{{/layout-section}}
--{{/layout}}

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@@ -1,1 +1,1 @@
--236824574
++235039398

URL

@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/236824574/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/235039398/14. Serial Crystallography: CFEL TapeDrive

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