Changes for page CFEL TapeDrive: Serial Crystallography

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

From 76.1 to 75.1 From 83.6 to 83.5

From version 83.5

edited by tabermah
on 2024-12-10 15:53

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To version 76.1

edited by ahenkel
on 2022-11-02 16:25

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Title

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

Author

@@ -1,1 +1,1 @@
--XWiki.tabermah
++XWiki.ahenkel

Content

@@ -3,28 +3,32 @@
  {{layout-cell}}
  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
++\\
--{{toc/}}
++{{toc minLevel="2"/}}
++\\
  ----
--= {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. Sample characteristics and preparation =
++== {{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.
++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 (green) or 50 µm (yellow) cell filter into an Eppendorf or Falcon (original!) tube
++* filter through 30 µm cell filter (green) or 50 µm (yellow)   into Eppendorf or Falcon (original!) tube
  [[image:attach:20211201_095534.jpg||height="250"]]
++\\
  ----
--= {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}8.2. 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 tube goes all the way 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!**
++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.
@@ -38,31 +38,30 @@
  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
++\\
  ----
--= {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. 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.
--
++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 ==
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
  * Click 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"]]
--[[image:attach:kamzik_tape.PNG||height="400"]]
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
--
--== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
--
  * Click on 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.
@@ -69,16 +69,16 @@
  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 the nozzle, 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
@@ -113,32 +113,38 @@
  be careful with -z, tape could be pushed out of focus
  )))
--
++**
++\\**
  )))
++* [[image:attach:kamzik_nozzle.PNG||height="400"]]
--[[image:attach:kamzik_nozzle.PNG||height="400"]]
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
--
--== {{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-Gasnozzle"/}}**Gas nozzle** ====
--== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
++\\
++==== {{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-14.4Taperollexchange"/}}8.4. Tape roll exchange =
++== {{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).
@@ -147,7 +147,7 @@
  * 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**. (% style="color: rgb(255,0,0);" %)//!!!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.
@@ -154,9 +154,15 @@
  * 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}}
@@ -164,19 +164,19 @@
  {{layout-cell}}
  ----
--= {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
  start chopper gui from terminal:
  (% class="code" %)
  (((
--            cd /gpfs/local/shared/ChopperControl
++            cd /gpfs/local/shared/ChopperControl
  )))
  (% class="code" %)
  (((
              python chopperControl.py
--\\
++\\\\
  )))
  {{/layout-cell}}
  {{/layout-section}}
@@ -189,17 +189,18 @@
  {{layout-cell}}
  **Chopper → no Chopper**
--* decrease frequency by max. 10 Hz steps
++* 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//
++* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
--(% style="color:#000000" %)**no Chopper → Chopper**
++(% style="color: rgb(0,0,0);" %)**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//
++* (% 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 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}}
@@ -207,7 +207,7 @@
  {{layout-cell}}
  ----
--= {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
++== {{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:
@@ -219,7 +219,7 @@
                                 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
--
++\\
  {{/layout-cell}}
  {{/layout-section}}
@@ -227,18 +227,23 @@
  {{layout-cell}}
  **Check list:**
--(% style="color:#ff0000" %)//always after entering the hutch!//
++(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
--(% style="color:#000000" %)Click "Run" icon in kamzik.
++(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
--* Put detector distance 200 in //prepare_for_measurement (      )//
--* Click "<Call>" next to //prepare_for_measurement//
--This will:
++* 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 //
++\\
++* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
++
++\\
++
  //**Set run parameters and go 🏃💥**//
 . Set your desired No. of frames
@@ -245,8 +245,9 @@
 . Enter the protein ID of your crystal sample
 . Match exposure time with chopper setting or set desired exposure time
 . Check trigger setting and match to chopper setting
--no chopper → external triffer //off//
--    chopper → external trigger// on//
++no chopper → external triffer //off
++//     chopper → external trigger// on
++//
 . To start the run, click "<Call>" next to //start_run (exposure    )//
  {{/layout-cell}}
@@ -257,7 +257,7 @@
  {{layout-section ac:type="single"}}
  {{layout-cell}}
--(% class="relative-table wrapped" style="width:55.9569%" %)
++(% class="relative-table wrapped" style="width: 55.9569%;" %)
  |=(((
  Parameter
  )))|=(((
@@ -279,7 +279,7 @@
  )))|(((
  exposure time of Eiger
--
++\\
  )))|(% colspan="1" %)(((
  with chopper         → opening time displayed in chopper GUI
  no chopper            → 7.7 ms
@@ -291,7 +291,7 @@
  )))|(((
  changes automatically
  )))|(% colspan="1" %)(((
--
++\\
  )))
  |(% colspan="1" %)(((
  Detector distance
@@ -298,7 +298,7 @@
  )))|(% colspan="1" %)(((
  current detector postion readout
  )))|(% colspan="1" %)(((
--
++\\
  )))
  |(% colspan="1" %)(((
  protein ID
@@ -305,7 +305,7 @@
  )))|(% colspan="1" %)(((
  protein ID of crystal sample (see AMARCORD)
  )))|(% colspan="1" %)(((
--
++\\
  )))
  ----
@@ -326,11 +326,15 @@
  {{/layout-cell}}
  {{layout-cell}}
--
++\\
++\\
++\\
++\\
++\\
  [[image:attach:safety_kamzik.PNG]]
  {{/layout-cell}}
@@ -340,17 +340,19 @@
  {{layout-cell}}
  ----
--= {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
  * (((
--== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
++==== {{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 ==
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
  * displayed in green=connected?
  * nozzle holder colliding somewhere?
@@ -357,8 +357,10 @@
  * motor limits reached? → position displayed in red
  )))
++\\
++
  * (((
--== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
++==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
  * channel turned on?
  * Sample empty?
@@ -365,21 +365,20 @@
  * Nozzle or lines clogged? → flush with water, change nozzle
  )))
++\\
++
  * (((
--== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
++==== {{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:*
--
--(((
++If nothing works, kill the Simplon process and then start the server again:* (((
  (% class="code" %)
  (((
  ssh haspp11exp03
  )))
  )))
--
  * (((
  (% class="code" %)
  (((
@@ -400,7 +400,7 @@
  {{layout-section ac:type="single"}}
  {{layout-cell}}
--
++\\
  {{/layout-cell}}
  {{/layout-section}}
  {{/layout}}

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Changes for page CFEL TapeDrive: Serial Crystallography

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