Changes for page CFEL TapeDrive: Serial Crystallography

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

From 50.1 to 49.1 From 69.1 to 68.1

From version 68.1

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

Change comment: There is no comment for this version

To version 50.1

edited by ahenkel
on 2022-04-04 19:18

Change comment: There is no comment for this version

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@@ -1,7 +1,7 @@
  {{layout}}
  {{layout-section ac:type="single"}}
  {{layout-cell}}
--[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
++[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
  \\
@@ -13,11 +13,11 @@
  == {{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) or 50 µm (yellow)   into Eppendorf or Falcon (original!) tube
++* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
  [[image:attach:20211201_095534.jpg||height="250"]]
@@ -57,7 +57,7 @@
  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-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.
@@ -66,7 +66,7 @@
  ==== {{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.
@@ -156,7 +156,7 @@
  * 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: rgb(255,0,0);" %)//!!!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.
@@ -214,13 +214,14 @@
  * (% 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 (technical exposure will always be 7.7 ms, since max. frame rate is 133 Hz
--//
++* (% 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-14.6Datacollection"/}}**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:
@@ -231,47 +231,60 @@
                        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_left_sidebar"}}
++{{layout-section ac:type="two_equal"}}
  {{layout-cell}}
  **Check list:**
  (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
--(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
++* 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)//
--* Put collimator in
--** Put detector distance 200 in //prepare_for_measurement (      )
--//
--** Click "<Call>" next to //prepare_for_measurement//
--
  \\
--* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
++**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//
++
  \\
--//**Set run parameters and go 🏃💥**//
++(% style="color: rgb(153,51,102);" %)**//Current bug~://**
--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);" %)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>".
--{{layout-cell}}
--[[image:attach:Kamzik_run(2).PNG||height="400"]]
++
++(% 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-section}}
--{{layout-section ac:type="two_equal"}}
  {{layout-cell}}
--(% class="relative-table" %)
++(% class="wrapped relative-table" style="width: 100.0%;" %)
  |=(((
  Parameter
  )))|=(((
@@ -295,7 +295,7 @@
  \\
  )))|(% colspan="1" %)(((
--chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
++chopper at 133 Hz → 3.7 ms
  chopper at 66 Hz   → 7.7 ms
@@ -324,19 +324,16 @@
  )))|(% 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"}}
@@ -371,41 +371,16 @@
  * 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
++* If nothing works, kill the Simplon process and then start the server again:
++** ssh haspp11exp03
++** ps -ef | grep Simplon
++** kill -9 simplon_process_id
  )))
--)))
--* (((
--(% 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 @@
--254729370
++250178622

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@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/254729370/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/250178622/14. Serial Crystallography: CFEL TapeDrive

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