Changes for page CFEL TapeDrive: Serial Crystallography

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

From 39.1 to 38.1 From 79.2 to 79.1

From version 79.1

edited by tabermah
on 2024-12-03 11:38

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To version 39.1

edited by ahenkel
on 2021-12-12 23:00

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Title

@@ -1,1 +1,1 @@
--08. Serial Crystallography: CFEL TapeDrive
++14. Serial Crystallography: CFEL TapeDrive

Author

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--XWiki.tabermah
++XWiki.ahenkel

Content

@@ -1,32 +1,83 @@
  {{layout}}
  {{layout-section ac:type="single"}}
  {{layout-cell}}
++
++
++{{toc/}}
++
  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
++\\
--{{toc minLevel="2"/}}
++\\
++\\
------
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
--== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**8.1 Sample characteristics and preparation** ==
++* 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
--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.
++(% 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.
--Preparation:
++\\
--* filter through 30 µm cell filter (green) or 50 µm (yellow)   into Eppendorf or Falcon (original!) tube
++* 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.
--[[image:attach:20211201_095534.jpg||height="250"]]
++\\
++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-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**8.2 Connecting sample to ElveFlow, sample exchange** ==
++\\
--*
--** ==
++=== {{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:
++
++* 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-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**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!**
  Be aware to which channel and nozzle line your sample is connected.
@@ -41,47 +41,44 @@
  [[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"/}}**8.3 TapeDrive operation** ==
--
--*
--** ==
--
--The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
++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** ====
++**Tape**
--* Click the 'main tape' icon
++* 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 on the 'nozzle' icon.
++* 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:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
++(% 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
++recommended step size
  for visual adjustment
  )))|=(% colspan="1" %)(((
  recommended step size
@@ -116,7 +116,8 @@
  be careful with -z, tape could be pushed out of focus
  )))
--
++**
++\\**
  )))
  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
@@ -124,23 +124,28 @@
  * 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)//
++                                        password: //written on control laptop (changes every 6 months)
++//
++\\
++\\
------
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
--== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**8.4 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.
@@ -148,7 +148,7 @@
  * 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**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
++* 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.
@@ -155,112 +155,63 @@
  * 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"]]**
++**[[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}}
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
--{{layout-section ac:type="single"}}
--{{layout-cell}}
------
++\\
--== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**8.5 Chopper** ==
++=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Datacollection"/}}**14.7 Data collection** ===
--start chopper gui from terminal:
++Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
--(% class="code" %)
--(((
--            cd /gpfs/local/shared/ChopperControl
--)))
++                                        xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
++                                        password: //written on control laptop (changes every 6 months)//
--(% class="code" %)
--(((
--            python chopperControl.py
--\\
--)))
--{{/layout-cell}}
--{{/layout-section}}
++                                           //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
--{{layout-section ac:type="two_equal"}}
--{{layout-cell}}
--                     [[image:attach:20211212_233140.jpg||height="250"]]
--{{/layout-cell}}
++\\
--{{layout-cell}}
--**Chopper → no Chopper**
++**Check list:**
--* 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:#ff0000" %)//Takes some minutes//
++* 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)//
--(% style="color:#000000" %)**no Chopper → Chopper**
++\\
--* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
--* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
--** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
--* (% style="color:#000000" %)//usually 130 Hz, results in exposure time of 3.7 ms (technical exposure will always be 7.7 ms, since max. frame rate is 130 Hz//
--{{/layout-cell}}
--{{/layout-section}}
++**Start run in kamzik
++**
--{{layout-section ac:type="single"}}
--{{layout-cell}}
------
++Click "Start" icon in kamzik.
--== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**8.6 Data collection** ==
++[[image:attach:kamzik_run-tile.jpg||height="400"]]
--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-tapetop
--                      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//
--
--
++----
  {{/layout-cell}}
  {{/layout-section}}
--{{layout-section ac:type="two_left_sidebar"}}
++{{layout-section ac:type="two_equal"}}
  {{layout-cell}}
--**Check list:**
++\\
--(% style="color:#ff0000" %)//always after entering the hutch!//
--
--(% style="color:#000000" %)Click "Run" icon in kamzik.
--
--* Put detector distance 200 in //prepare_for_measurement (      )//
--* Click "<Call>" next to //prepare_for_measurement//
--This will:
--** drive the collimator in //IN// position
--** drive detector to 200 mm
--
--* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
--
--//**Set run parameters and go 🏃💥**//
--
 . Set your desired No. of frames
--1. Enter the protein ID of your crystal sample
--1. Match exposure time with chopper setting or set desired exposure time
++1. Match exposure time with chopper setting
 . Check trigger setting and match to chopper setting
--no chopper → external triffer //off//
--    chopper → external trigger// on//
--1. To start the run, click "<Call>" next to //start_run (exposure    )//
++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//
  {{/layout-cell}}
  {{layout-cell}}
--[[image:attach:Kamzik_run(2).PNG]]
--{{/layout-cell}}
--{{/layout-section}}
--
--{{layout-section ac:type="single"}}
--{{layout-cell}}
--(% class="relative-table wrapped" style="width:55.9569%" %)
++(% class="wrapped" %)
  |=(((
  Parameter
  )))|=(((
@@ -271,7 +271,7 @@
  |(((
  Images number
  )))|(((
--number of frames you want to collect
++Set number of frames you want to collect
  )))|(% colspan="1" %)(((
  usually 100k - 200k, but adjust according to hitrate
@@ -282,9 +282,12 @@
  )))|(((
  exposure time of Eiger
--
++\\
  )))|(% colspan="1" %)(((
--with chopper         → opening time displayed in chopper GUI
++chopper at 133 Hz → 3.7 ms
++
++chopper at 66 Hz   → 7.7 ms
++
  no chopper            → 7.7 ms
  ----
@@ -294,7 +294,7 @@
  )))|(((
  changes automatically
  )))|(% colspan="1" %)(((
--
++\\
  )))
  |(% colspan="1" %)(((
  Detector distance
@@ -301,109 +301,38 @@
  )))|(% colspan="1" %)(((
  current detector postion readout
  )))|(% colspan="1" %)(((
--
++\\
  )))
  |(% colspan="1" %)(((
--protein ID
++move_detector (distance)
  )))|(% colspan="1" %)(((
--protein ID of crystal sample (see AMARCORD)
++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!!!**
++)))
  {{/layout-cell}}
  {{/layout-section}}
--{{layout-section ac:type="two_equal"}}
--{{layout-cell}}
--**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]]
--{{/layout-cell}}
--
--{{layout-cell}}
--
--
--
--
--
--
--[[image:attach:safety_kamzik.PNG]]
--{{/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-14.7Troubleshooting"/}}**8.7 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
--)))
--)))
--)))
--* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
--)))
  {{/layout-cell}}
  {{/layout-section}}
--
--{{layout-section ac:type="single"}}
--{{layout-cell}}
--
--{{/layout-cell}}
--{{/layout-section}}
  {{/layout}}

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Confluence.Code.ConfluencePageClass[0]

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--235031805
++236824573

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--https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/236824573/14. Serial Crystallography: CFEL TapeDrive

Changes for page CFEL TapeDrive: Serial Crystallography

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