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Last modified by chatzies on 2025-11-27 11:35
From version 46.1
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  
... ... @@ -9,18 +9,22 @@
9 9  
10 10  \\
11 11  
12 +----
13 +
12 12  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
13 13  
14 -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.
15 15  
16 16  Preparation:
17 17  
18 -* 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
19 19  
20 20  [[image:attach:20211201_095534.jpg||height="250"]]
21 21  
22 22  \\
23 23  
26 +----
27 +
24 24  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
25 25  ** ==
26 26  
... ... @@ -40,6 +40,8 @@
40 40  
41 41  \\
42 42  
47 +----
48 +
43 43  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
44 44  ** ==
45 45  
... ... @@ -51,7 +51,7 @@
51 51  
52 52  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
53 53  
54 -* Click on the 'main tape' icon
60 +* Click the 'main tape' icon
55 55  * Change the velocity by typing anything from **0.3-3.0 mm/s**
56 56  * Common velocity is 1.0-1.5 mm/s
57 57  * 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.
... ... @@ -60,7 +60,7 @@
60 60  
61 61  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
62 62  
63 -* Click an the 'nozzle' icon.
69 +* Click on the 'nozzle' icon.
64 64  * (((
65 65  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.
66 66  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
... ... @@ -139,8 +139,10 @@
139 139  
140 140  \\
141 141  
142 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ==
148 +----
143 143  
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151 +
144 144  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).
145 145  
146 146  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -148,7 +148,7 @@
148 148  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
149 149  * Cut the first cm of the new tape roll, directly behind the black sticky part.
150 150  * 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.
151 -* 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!!!//
152 152  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
153 153  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
154 154  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -162,15 +162,17 @@
162 162  
163 163  \\
164 164  
165 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
166 -** ===
173 +**
174 +**
167 167  {{/layout-cell}}
168 168  {{/layout-section}}
169 169  
170 170  {{layout-section ac:type="single"}}
171 171  {{layout-cell}}
172 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ==
180 +----
173 173  
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183 +
174 174  start chopper gui from terminal:
175 175  
176 176  (% class="code" %)
... ... @@ -181,6 +181,7 @@
181 181  (% class="code" %)
182 182  (((
183 183   python chopperControl.py
194 +\\\\
184 184  )))
185 185  {{/layout-cell}}
186 186  {{/layout-section}}
... ... @@ -203,76 +203,72 @@
203 203  * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
204 204  * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
205 205  ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
206 -* (% 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 +//
207 207  {{/layout-cell}}
208 208  {{/layout-section}}
209 209  
210 210  {{layout-section ac:type="single"}}
211 211  {{layout-cell}}
212 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ==
224 +----
213 213  
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227 +
214 214  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
215 215  
216 216  (% class="code" %)
217 217  (((
218 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
232 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
219 219   password: written on control laptop (changes every 6 months)
220 220  )))
221 221  
222 - //>>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//
223 223  
224 224  \\
225 -
226 -Click "Start" icon in kamzik.
227 -
228 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
229 -
230 -----
231 231  {{/layout-cell}}
232 232  {{/layout-section}}
233 233  
234 -{{layout-section ac:type="two_equal"}}
242 +{{layout-section ac:type="two_left_sidebar"}}
235 235  {{layout-cell}}
236 236  **Check list:**
237 237  
238 238  (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
239 239  
240 -* Open BS1  (//CrystalControl)//
241 -* Put collimator in (//CrystalControl)//
242 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
243 -* Open fast shutter (//CrystalControl)//
244 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
245 -* Close fast shutter (//CrystalControl)//
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
246 246  
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 +
247 247  \\
248 248  
249 -**Set run parameters and go 🏃💥**
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
250 250  
251 -1. Set your desired No. of frames
252 -1. Match exposure time with chopper setting
253 -1. Check trigger setting and match to chopper setting
254 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
255 -1. To start the run, click "<Call>" next to //exposure time//
256 -
257 257  \\
258 258  
259 -(% style="color: rgb(153,51,102);" %)**//Current bug~://**
263 +//**Set run parameters and go 🏃💥**//
260 260  
261 -(% 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}}
262 262  
263 -
264 -(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
265 -
266 -(% class="code" %)
267 -(((
268 - cd /gpfs/current/raw/scan_frames
269 - watch "ls -lrt <run number>/ | tail"
270 -\\\\\\\\
271 -)))
275 +{{layout-cell}}
276 +[[image:attach:Kamzik_run(2).PNG]]
272 272  {{/layout-cell}}
278 +{{/layout-section}}
273 273  
280 +{{layout-section ac:type="single"}}
274 274  {{layout-cell}}
275 -(% class="wrapped relative-table" style="width: 100.0%;" %)
282 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
276 276  |=(((
277 277  Parameter
278 278  )))|=(((
... ... @@ -283,7 +283,7 @@
283 283  |(((
284 284  Images number
285 285  )))|(((
286 -Set number of frames you want to collect
293 +number of frames you want to collect
287 287  )))|(% colspan="1" %)(((
288 288  usually 100k - 200k, but adjust according to hitrate
289 289  
... ... @@ -296,10 +296,7 @@
296 296  
297 297  \\
298 298  )))|(% colspan="1" %)(((
299 -chopper at 133 Hz → 3.7 ms
300 -
301 -chopper at 66 Hz   → 7.7 ms
302 -
306 +with chopper         → opening time displayed in chopper GUI
303 303  no chopper            → 7.7 ms
304 304  
305 305  ----
... ... @@ -319,29 +319,50 @@
319 319  \\
320 320  )))
321 321  |(% colspan="1" %)(((
322 -move_detector (distance)
326 +protein ID
323 323  )))|(% colspan="1" %)(((
324 -Set detector distance
328 +protein ID of crystal sample (see AMARCORD)
325 325  )))|(% colspan="1" %)(((
326 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
330 +\\
327 327  )))
328 -|(% colspan="1" %)(((
329 -Diode voltage
330 -)))|(% colspan="1" %)(((
331 -read out of diode
332 -)))|(% colspan="1" %)(((
333 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 
334 -Call local contact
335 -**
336 -)))
332 +
333 +----
337 337  {{/layout-cell}}
338 338  {{/layout-section}}
339 339  
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 +
340 340  {{layout-section ac:type="single"}}
341 341  {{layout-cell}}
342 342  ----
343 343  
344 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}**14.9 Troubleshooting** ==
369 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
345 345  
346 346  * (((
347 347  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -369,6 +369,42 @@
369 369  * Sample empty?
370 370  * Nozzle or lines clogged? → flush with water, change nozzle
371 371  )))
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 +)))
372 372  {{/layout-cell}}
373 373  {{/layout-section}}
429 +
430 +{{layout-section ac:type="single"}}
431 +{{layout-cell}}
432 +\\
433 +{{/layout-cell}}
434 +{{/layout-section}}
374 374  {{/layout}}
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1 +235031805
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1 -https://confluence.desy.de/spaces/11/pages/236824598/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive