Changes for page CFEL TapeDrive: Serial Crystallography

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

From 48.1 to 49.1 From 63.1 to 64.1

From version 49.1

edited by ahenkel
on 2022-04-04 14:43

Change comment: There is no comment for this version

To version 63.1

edited by ahenkel
on 2022-04-19 14:19

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="250"]]
++[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
  \\
@@ -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) 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"]]
@@ -57,7 +57,7 @@
  ==== {{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.
@@ -66,7 +66,7 @@
  ==== {{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.
@@ -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**. //!!!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.
@@ -220,8 +220,6 @@
  {{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:
@@ -232,33 +232,47 @@
                        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 "Safety" icon in kamzik.
++* Put collimator in
++** Click "<Call>" next to //collimator_in//
++
  \\
++* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
++{{/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 🏃💥**
 . Set your desired No. of frames
@@ -269,19 +269,17 @@
  \\
--(% style="color: rgb(153,51,102);" %)**//Current bug~://**
++\\
--(% 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>".
++**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).
--(% 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"
--\\\\\\\\
--)))
++[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
  {{/layout-cell}}
  {{layout-cell}}
@@ -382,16 +382,41 @@
  * 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:
--** ssh haspp11exp03
--** ps -ef | grep Simplon
--** kill -9 simplon_process_id
++* (((
++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}}

Confluence.Code.ConfluencePageClass[0]

Id

@@ -1,1 +1,1 @@
--250178591
++252826012

URL

@@ -1,1 +1,1 @@
--https://confluence.desy.de/spaces/11/pages/250178591/14. Serial Crystallography: CFEL TapeDrive
++https://confluence.desy.de/spaces/11/pages/252826012/14. Serial Crystallography: CFEL TapeDrive

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