Changes for page CFEL TapeDrive: Serial Crystallography

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

From 24.1 to 25.1 From 45.1 to 46.1

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edited by ahenkel
on 2021-12-03 11:34

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edited by ahenkel
on 2021-12-12 23:53

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@@ -1,67 +1,14 @@
++{{layout}}
++{{layout-section ac:type="single"}}
++{{layout-cell}}
++[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
--
--{{toc/}}
--
--[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
--
  \\
  \\
--\\
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
--=== {{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)
--* move cryojet out of the way, ramp the cryo up and shut it down. Close the compressed air to the shield flow. The biggest cable kinks and needs to be disconnected.
--* stop refill of the robot dewar and empty the dewar, warm up.
--* Disable backlight (unplug Festo connection). (% style="color: rgb(255,0,0);" %)//Is this still needed?//
--* (% style="color: rgb(0,0,0);" %)mount the 10 um diode and connect (via connector on the granite). This is connected to the leftmost Keithly (power up, check that settings are gain E06, Filter on, Rise time 1 ms. Keithly is connected to the oscilloscope and the delay generator, delay generator is connected to oscilloscope and detector, see diagram in P11 wiki. (% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)//Insert here the setting for oscilloscope//(% style="color: rgb(0,0,0);" %)//. //Make sure to connect the multi-trigger to the back of the detector instead of the standard trigger, when starting to use the chopper (pull the thin ring with ‘grip’ area to detach). Cables are labeled. Make sure before using the chopper that the channels are enabled.
--* (% style="color: rgb(0,0,0);" %)move goniotower to X ~~ 17 000
--
--(% style="color: rgb(0,0,0);" %)Mounting of the TapeDrive is done by the CFEL group. Electronics and control units are combined on a small shelf, that requires only one power and network plug-in. The shelf will be placed left-sided (looking upstream) to the detector tower. The ElveFlow and control laptop as well as several necessary consumables are placed on a cart, which is to be positioned on the right (looking upstream) against the robot platform. The CFEL chiller is placed on the right of the platform and connected to the TapeDrive GASnozzle.
--
--\\
--
--* adjust focus of the tape by moving X in goniometer tower until you see it in the overview camera. Final adjustment should be done when there is flow. Latest value is about 4500 in X and also 5000 in Z (higher soft limit changed from 2976,63 to 6000). (% style="color: rgb(255,0,0);" %)//Better to use the back illumination in the GUI to focus the tape - old instruction, not sure if this is the case. Back illumination is the external light source in the detector tower (the crystallography backlight should be disable for tapedrive).//
--* (% style="color: rgb(0,0,0);" %)Check the Minimum Detector Distance; the detector should not collide with the tapedrive while driven to 154 mm but it has to be verified. Also check that all cables and capillaries are taped away when the users start, so that nothing protrudes further than the tapedrive itself. Soft limit can be edited in eh.3.11 Atk panel.
--* (% style="color: rgb(0,0,0);" %)Reconfirm the alignment of the beamstop, once everything, including the nozzle, is in place. Modify config.ini for beamstop in- and out-position to both mach in (27 000). This way the beamstop will not be driven out when the hutch is opened, to avoid that the users forget to drive it in when restarting after entering the hutch.
--
--\\
--
--Prepare necessary controls for data collection:
--
--* ATK panels:
--** p11/simplon_filewriter/eh.01
--** p11/simplon_detector/eh.01
--*** count time = 0.0075
--*** trigger (**ints **if working without the chopper, # or triggers is 1, **exts** if with the chopper, # or triggers = number of images). Exts is also the standard trigger in normal crystallography. If GUI is used to take images (e.g. for beamstop alignment) the trigger mode will be forced by that and needs to be reverted manually for the users to continue.
--*** numer of images = 100 000
--*** number of images in container = 1000
--*** mode 16m/4M
--*** detector distance = 200 mm (usually)
--** p11/detectortower
--** p11/motor/eh.09
--* remote access to TapeDrive control laptop:
--** open terminal, execute command:          xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
--                                                             password: //written on control laptop
--//
--* Cameras:
--** haspp11ethcam1 → detector tower camera to monitor nozzle
--** haspp11ethcam4 →  goniometer camera to monitor tape from above
--* OnDa (on haspp11user04):
--//This starts both GUIs (Frame Viewer & Crystallography GUI) and onda-monitor, the server component. The tool has a bunch of parameters which you can list with ./onda-runner.py —help.//\\
--** 16M mode →    cd /home/p11user/CfelSoft/202103_onda
--                         ./onda-runner.py onda-config/onda-config-Eiger16M.toml
--** 4M mode   →    cd /home/p11user/CfelSoft/202103_onda
--                         ./onda-runner.py onda-config/onda-config-Eiger4M.toml\\
--
--\\
--
--=== {{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.
  Preparation:
@@ -72,25 +72,27 @@
  \\
--=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
--** ===
++== {{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)
++            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
--** ===
++== {{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.
@@ -98,7 +98,7 @@
  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**
++==== {{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**
@@ -107,15 +107,17 @@
  \\
  * [[image:attach:kamzik_tape.PNG||height="400"]]
--==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle:"/}}**Sample nozzle:** ====
++==== {{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.
++
++(% 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" %)
  |=(((
  \\
@@ -164,12 +164,16 @@
  ==== {{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:
@@ -182,7 +182,7 @@
  \\
--==== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ====
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**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).
@@ -189,15 +189,16 @@
  * 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 before the black sticky part.
--* Use this sticky part to attach the end of the old tape to the new roll. Place new roll on roll holder.
--* Open magnetic tape stabilizer.
--* Start the tape (3mm/s). Once the connetion side (black sticky part) has arrived at the collector roll, stop the tape (0mm/s).
--* Again, cut the tape directly in front of the black mark. Replace the the old roll with the **empty **one. Old roll can be discarded.
--* Attach new tape to the empty roll by using the black sticky part.
++* 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:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
  **
  \\
@@ -204,8 +204,213 @@
  \\
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
++** ===
++{{/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 @@
--235039466
++236824595

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@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/235039466/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/236824595/14. Serial Crystallography: CFEL TapeDrive

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