Changes for page CFEL TapeDrive: Serial Crystallography

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

From 44.1 to 45.1 From 68.1 to 69.1

From version 45.1

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

Change comment: There is no comment for this version

To version 68.1

edited by ahenkel
on 2022-05-07 18:53

Change comment: There is no comment for this version

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@@ -1,24 +1,30 @@
  {{layout}}
  {{layout-section ac:type="single"}}
  {{layout-cell}}
--[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
++[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
  \\
++{{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.
++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
++* 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"/}}**14.2 Connecting sample to ElveFlow, sample exchange
  ** ==
@@ -38,6 +38,8 @@
  \\
++----
++
  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
  ** ==
@@ -49,7 +49,7 @@
  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
--* Click on the 'main tape' icon
++* 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.
@@ -58,7 +58,7 @@
  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
--* Click an the 'nozzle' icon.
++* 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.
  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
@@ -137,8 +137,10 @@
  \\
--== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 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).
  * Remove the (almost) empty feeder roll by pulling it upwards.
@@ -146,7 +146,7 @@
  * 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**. //!!!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.
@@ -160,15 +160,17 @@
  \\
--=== {{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** ==
++----
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
++
  start chopper gui from terminal:
  (% class="code" %)
@@ -179,6 +179,7 @@
  (% class="code" %)
  (((
              python chopperControl.py
++\\\\
  )))
  {{/layout-cell}}
  {{/layout-section}}
@@ -201,13 +201,14 @@
  * (% 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//
++* (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms (technical exposure will always be 7.7 ms, since max. frame rate is 133 Hz
++//
  {{/layout-cell}}
  {{/layout-section}}
  {{layout-section ac:type="single"}}
  {{layout-cell}}
--== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 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:
@@ -217,60 +217,47 @@
                        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//
++                               //>>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-section ac:type="two_left_sidebar"}}
  {{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)//
++(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
++* Put collimator in
++** Put detector distance 200 in //prepare_for_measurement (      )
++//
++** Click "<Call>" next to //prepare_for_measurement//
++
  \\
--**Set run parameters and go 🏃💥**
++* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
--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~://**
++//**Set run parameters and go 🏃💥**//
--(% 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>".
++1. Set your desired No. of frames
++1. Match exposure time with chopper setting or set desired exposure time
++1. Check trigger setting and match to chopper setting
++1. To start the run, click "<Call>" next to //start_run (exposure    )//
++{{/layout-cell}}
--
--(% 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}}
++[[image:attach:Kamzik_run(2).PNG||height="400"]]
  {{/layout-cell}}
++{{/layout-section}}
++{{layout-section ac:type="two_equal"}}
  {{layout-cell}}
--(% class="wrapped relative-table" style="width: 100.0%;" %)
++(% class="relative-table" %)
  |=(((
  Parameter
  )))|=(((
@@ -294,7 +294,7 @@
  \\
  )))|(% colspan="1" %)(((
--chopper at 133 Hz → 3.7 ms
++chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
  chopper at 66 Hz   → 7.7 ms
@@ -323,16 +323,19 @@
  )))|(% colspan="1" %)(((
 .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-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||height="400"]]
++{{/layout-cell}}
  {{/layout-section}}
  {{layout-section ac:type="single"}}
@@ -339,7 +339,7 @@
  {{layout-cell}}
  ----
--== {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}**14.9 Troubleshooting** ==
++== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
  * (((
  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
@@ -367,6 +367,41 @@
  * 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 @@
--236824595
++254729370

URL

@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/236824595/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/254729370/14. Serial Crystallography: CFEL TapeDrive

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