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Last modified by chatzies on 2025-11-27 11:35
From version 45.1
edited by ahenkel
on 2021-12-12 23:53
Change comment: There is no comment for this version
To version 76.1
edited by ahenkel
on 2022-11-02 16:25
Change comment: There is no comment for this version

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1 1  {{layout}}
2 2  {{layout-section ac:type="single"}}
3 3  {{layout-cell}}
4 -[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 6  \\
7 7  
8 +{{toc minLevel="2"/}}
9 +
8 8  \\
9 9  
12 +----
13 +
10 10  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
11 11  
12 -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.
16 +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.
13 13  
14 14  Preparation:
15 15  
16 -* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
20 +* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
17 17  
18 18  [[image:attach:20211201_095534.jpg||height="250"]]
19 19  
20 20  \\
21 21  
26 +----
27 +
22 22  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
23 23  ** ==
24 24  
... ... @@ -38,6 +38,8 @@
38 38  
39 39  \\
40 40  
47 +----
48 +
41 41  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
42 42  ** ==
43 43  
... ... @@ -49,7 +49,7 @@
49 49  
50 50  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
51 51  
52 -* Click on the 'main tape' icon
60 +* Click the 'main tape' icon
53 53  * Change the velocity by typing anything from **0.3-3.0 mm/s**
54 54  * Common velocity is 1.0-1.5 mm/s
55 55  * 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 @@
58 58  
59 59  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
60 60  
61 -* Click an the 'nozzle' icon.
69 +* Click on the 'nozzle' icon.
62 62  * (((
63 63  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.
64 64  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
... ... @@ -137,8 +137,10 @@
137 137  
138 138  \\
139 139  
140 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ==
148 +----
141 141  
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151 +
142 142  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).
143 143  
144 144  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -146,7 +146,7 @@
146 146  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
147 147  * Cut the first cm of the new tape roll, directly behind the black sticky part.
148 148  * 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.
149 -* Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
150 150  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
151 151  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
152 152  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -160,15 +160,17 @@
160 160  
161 161  \\
162 162  
163 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
164 -** ===
173 +**
174 +**
165 165  {{/layout-cell}}
166 166  {{/layout-section}}
167 167  
168 168  {{layout-section ac:type="single"}}
169 169  {{layout-cell}}
170 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ==
180 +----
171 171  
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183 +
172 172  start chopper gui from terminal:
173 173  
174 174  (% class="code" %)
... ... @@ -179,6 +179,7 @@
179 179  (% class="code" %)
180 180  (((
181 181   python chopperControl.py
194 +\\\\
182 182  )))
183 183  {{/layout-cell}}
184 184  {{/layout-section}}
... ... @@ -201,76 +201,72 @@
201 201  * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
202 202  * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
203 203  ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
204 -* (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
217 +* (% 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
218 +//
205 205  {{/layout-cell}}
206 206  {{/layout-section}}
207 207  
208 208  {{layout-section ac:type="single"}}
209 209  {{layout-cell}}
210 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ==
224 +----
211 211  
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227 +
212 212  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
213 213  
214 214  (% class="code" %)
215 215  (((
216 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
232 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
217 217   password: written on control laptop (changes every 6 months)
218 218  )))
219 219  
220 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
236 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
221 221  
222 222  \\
223 -
224 -Click "Start" icon in kamzik.
225 -
226 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
227 -
228 -----
229 229  {{/layout-cell}}
230 230  {{/layout-section}}
231 231  
232 -{{layout-section ac:type="two_equal"}}
242 +{{layout-section ac:type="two_left_sidebar"}}
233 233  {{layout-cell}}
234 234  **Check list:**
235 235  
236 236  (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
237 237  
238 -* Open BS1  (//CrystalControl)//
239 -* Put collimator in (//CrystalControl)//
240 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
241 -* Open fast shutter (//CrystalControl)//
242 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
243 -* Close fast shutter (//CrystalControl)//
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
244 244  
250 +* Put detector distance 200 in //prepare_for_measurement (      )
251 +//
252 +* Click "<Call>" next to //prepare_for_measurement
253 +//This will:\\
254 +** drive the collimator in //IN// position
255 +** drive detector to 200 mm
256 +
245 245  \\
246 246  
247 -**Set run parameters and go 🏃💥**
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
248 248  
249 -1. Set your desired No. of frames
250 -1. Match exposure time with chopper setting
251 -1. Check trigger setting and match to chopper setting
252 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
253 -1. To start the run, click "<Call>" next to //exposure time//
254 -
255 255  \\
256 256  
257 -(% style="color: rgb(153,51,102);" %)**//Current bug~://**
263 +//**Set run parameters and go 🏃💥**//
258 258  
259 -(% 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>".
265 +1. Set your desired No. of frames
266 +1. Enter the protein ID of your crystal sample
267 +1. Match exposure time with chopper setting or set desired exposure time
268 +1. Check trigger setting and match to chopper setting
269 +no chopper → external triffer //off
270 +// chopper → external trigger// on
271 +//
272 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
273 +{{/layout-cell}}
260 260  
261 -
262 -(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
263 -
264 -(% class="code" %)
265 -(((
266 - cd /gpfs/current/raw/scan_frames
267 - watch "ls -lrt <run number>/ | tail"
268 -\\\\\\\\
269 -)))
275 +{{layout-cell}}
276 +[[image:attach:Kamzik_run(2).PNG]]
270 270  {{/layout-cell}}
278 +{{/layout-section}}
271 271  
280 +{{layout-section ac:type="single"}}
272 272  {{layout-cell}}
273 -(% class="wrapped relative-table" style="width: 100.0%;" %)
282 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
274 274  |=(((
275 275  Parameter
276 276  )))|=(((
... ... @@ -281,7 +281,7 @@
281 281  |(((
282 282  Images number
283 283  )))|(((
284 -Set number of frames you want to collect
293 +number of frames you want to collect
285 285  )))|(% colspan="1" %)(((
286 286  usually 100k - 200k, but adjust according to hitrate
287 287  
... ... @@ -294,10 +294,7 @@
294 294  
295 295  \\
296 296  )))|(% colspan="1" %)(((
297 -chopper at 133 Hz → 3.7 ms
298 -
299 -chopper at 66 Hz   → 7.7 ms
300 -
306 +with chopper         → opening time displayed in chopper GUI
301 301  no chopper            → 7.7 ms
302 302  
303 303  ----
... ... @@ -317,29 +317,50 @@
317 317  \\
318 318  )))
319 319  |(% colspan="1" %)(((
320 -move_detector (distance)
326 +protein ID
321 321  )))|(% colspan="1" %)(((
322 -Set detector distance
328 +protein ID of crystal sample (see AMARCORD)
323 323  )))|(% colspan="1" %)(((
324 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
330 +\\
325 325  )))
326 -|(% colspan="1" %)(((
327 -Diode voltage
328 -)))|(% colspan="1" %)(((
329 -read out of diode
330 -)))|(% colspan="1" %)(((
331 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 
332 -Call local contact
333 -**
334 -)))
332 +
333 +----
335 335  {{/layout-cell}}
336 336  {{/layout-section}}
337 337  
337 +{{layout-section ac:type="two_equal"}}
338 +{{layout-cell}}
339 +**After data collection/Before entering the exp. hutch:**
340 +
341 +1. Go to "Safety" in kamzik.
342 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
343 +11. Drive the collimator out
344 +11. Drive the detector back to 1500 mm
345 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
346 +
347 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
348 +{{/layout-cell}}
349 +
350 +{{layout-cell}}
351 +\\
352 +
353 +\\
354 +
355 +\\
356 +
357 +\\
358 +
359 +\\
360 +
361 +[[image:attach:safety_kamzik.PNG]]
362 +{{/layout-cell}}
363 +{{/layout-section}}
364 +
338 338  {{layout-section ac:type="single"}}
339 339  {{layout-cell}}
340 340  ----
341 341  
342 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}**14.9 Troubleshooting** ==
369 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
343 343  
344 344  * (((
345 345  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -367,6 +367,42 @@
367 367  * Sample empty?
368 368  * Nozzle or lines clogged? → flush with water, change nozzle
369 369  )))
397 +
398 +\\
399 +
400 +* (((
401 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
402 +
403 +* First, restart kamzik (server+client) and see if this solves the issue
404 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
405 +* (((
406 +If nothing works, kill the Simplon process and then start the server again:* (((
407 +(% class="code" %)
408 +(((
409 +ssh haspp11exp03
410 +)))
411 +)))
412 +* (((
413 +(% class="code" %)
414 +(((
415 +ps -ef | grep Simplon
416 +)))
417 +)))
418 +* (((
419 +(% class="code" %)
420 +(((
421 +kill -9 simplon_process_id
422 +)))
423 +)))
424 +)))
425 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
426 +)))
370 370  {{/layout-cell}}
371 371  {{/layout-section}}
429 +
430 +{{layout-section ac:type="single"}}
431 +{{layout-cell}}
432 +\\
433 +{{/layout-cell}}
434 +{{/layout-section}}
372 372  {{/layout}}
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1 -https://confluence.desy.de/spaces/11/pages/236824595/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive