Changes for page CFEL TapeDrive: Serial Crystallography

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

From 3.1 to 2.1 From 52.1 to 51.1

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edited by ahenkel
on 2022-04-04 19:45

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To version 3.1

edited by ahenkel
on 2021-11-30 10:55

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@@ -1,428 +1,3 @@
--{{layout}}
--{{layout-section ac:type="single"}}
--{{layout-cell}}
--[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
++**14.1 Revert from Crystallography to TapeDrive (P11 staff)**
  \\
--
--{{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}}

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@@ -1,1 +1,1 @@
--250178623
++235032181

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@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/250178623/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/235032181/14. Serial Crystallography: CFEL TapeDrive

Changes for page CFEL TapeDrive: Serial Crystallography

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