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Last modified by chatzies on 2025-11-27 11:35
From version 76.1
edited by ahenkel
on 2022-11-02 16:25
Change comment: There is no comment for this version
To version 49.1
edited by ahenkel
on 2022-04-04 14:43
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="400"]]
4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
5 5  
6 6  \\
7 7  
... ... @@ -13,11 +13,11 @@
13 13  
14 14  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
15 15  
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.
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.
17 17  
18 18  Preparation:
19 19  
20 -* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
20 +* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
21 21  
22 22  [[image:attach:20211201_095534.jpg||height="250"]]
23 23  
... ... @@ -57,7 +57,7 @@
57 57  
58 58  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
59 59  
60 -* Click the 'main tape' icon
60 +* Click on the 'main tape' icon
61 61  * Change the velocity by typing anything from **0.3-3.0 mm/s**
62 62  * Common velocity is 1.0-1.5 mm/s
63 63  * 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 @@
66 66  
67 67  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
68 68  
69 -* Click on the 'nozzle' icon.
69 +* Click an the 'nozzle' icon.
70 70  * (((
71 71  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.
72 72  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
... ... @@ -156,7 +156,7 @@
156 156  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
157 157  * Cut the first cm of the new tape roll, directly behind the black sticky part.
158 158  * 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.
159 -* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
160 160  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
161 161  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
162 162  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -214,8 +214,7 @@
214 214  * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
215 215  * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
216 216  ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
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 -//
217 +* (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
219 219  {{/layout-cell}}
220 220  {{/layout-section}}
221 221  
... ... @@ -229,57 +229,64 @@
229 229  
230 230  (% class="code" %)
231 231  (((
232 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
231 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
233 233   password: written on control laptop (changes every 6 months)
234 234  )))
235 235  
236 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
235 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
237 237  
238 238  \\
238 +
239 +Click "Start" icon in kamzik.
240 +
241 +[[image:attach:kamzik_run-tile.jpg||height="400"]]
242 +
243 +----
239 239  {{/layout-cell}}
240 240  {{/layout-section}}
241 241  
242 -{{layout-section ac:type="two_left_sidebar"}}
247 +{{layout-section ac:type="two_equal"}}
243 243  {{layout-cell}}
244 244  **Check list:**
245 245  
246 246  (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
247 247  
248 -(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
253 +* Open BS1  (//CrystalControl)//
254 +* Put collimator in (//CrystalControl)//
255 +* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
256 +* Open fast shutter (//CrystalControl)//
257 +* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
258 +* Close fast shutter (//CrystalControl)//
249 249  
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 -
257 257  \\
258 258  
259 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
262 +**Set run parameters and go 🏃💥**
260 260  
264 +1. Set your desired No. of frames
265 +1. Match exposure time with chopper setting
266 +1. Check trigger setting and match to chopper setting
267 +1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
268 +1. To start the run, click "<Call>" next to //exposure time//
269 +
261 261  \\
262 262  
263 -//**Set run parameters and go 🏃💥**//
272 +(% style="color: rgb(153,51,102);" %)**//Current bug~://**
264 264  
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}}
274 +(% 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>".
274 274  
275 -{{layout-cell}}
276 -[[image:attach:Kamzik_run(2).PNG]]
276 +
277 +(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
278 +
279 +(% class="code" %)
280 +(((
281 + cd /gpfs/current/raw/scan_frames
282 + watch "ls -lrt <run number>/ | tail"
283 +\\\\\\\\
284 +)))
277 277  {{/layout-cell}}
278 -{{/layout-section}}
279 279  
280 -{{layout-section ac:type="single"}}
281 281  {{layout-cell}}
282 -(% class="relative-table wrapped" style="width: 55.9569%;" %)
288 +(% class="wrapped relative-table" style="width: 100.0%;" %)
283 283  |=(((
284 284  Parameter
285 285  )))|=(((
... ... @@ -290,7 +290,7 @@
290 290  |(((
291 291  Images number
292 292  )))|(((
293 -number of frames you want to collect
299 +Set number of frames you want to collect
294 294  )))|(% colspan="1" %)(((
295 295  usually 100k - 200k, but adjust according to hitrate
296 296  
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303 303  
304 304  \\
305 305  )))|(% colspan="1" %)(((
306 -with chopper         → opening time displayed in chopper GUI
312 +chopper at 133 Hz → 3.7 ms
313 +
314 +chopper at 66 Hz   → 7.7 ms
315 +
307 307  no chopper            → 7.7 ms
308 308  
309 309  ----
... ... @@ -323,45 +323,24 @@
323 323  \\
324 324  )))
325 325  |(% colspan="1" %)(((
326 -protein ID
335 +move_detector (distance)
327 327  )))|(% colspan="1" %)(((
328 -protein ID of crystal sample (see AMARCORD)
337 +Set detector distance
329 329  )))|(% colspan="1" %)(((
330 -\\
339 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
331 331  )))
332 -
333 -----
341 +|(% colspan="1" %)(((
342 +Diode voltage
343 +)))|(% colspan="1" %)(((
344 +read out of diode
345 +)))|(% colspan="1" %)(((
346 +**~~ 0 !!! higher values indicate missaligned beam stop!!! 
347 +Call local contact
348 +**
349 +)))
334 334  {{/layout-cell}}
335 335  {{/layout-section}}
336 336  
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 -
365 365  {{layout-section ac:type="single"}}
366 366  {{layout-cell}}
367 367  ----
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394 394  * Sample empty?
395 395  * Nozzle or lines clogged? → flush with water, change nozzle
396 396  )))
397 -
398 -\\
399 -
400 400  * (((
401 401  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
402 402  
403 403  * First, restart kamzik (server+client) and see if this solves the issue
404 404  * 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
390 +* If nothing works, kill the Simplon process and then start the server again:
391 +** ssh haspp11exp03
392 +** ps -ef | grep Simplon
393 +** kill -9 simplon_process_id
410 410  )))
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 -)))
427 427  {{/layout-cell}}
428 428  {{/layout-section}}
429 -
430 -{{layout-section ac:type="single"}}
431 -{{layout-cell}}
432 -\\
433 -{{/layout-cell}}
434 -{{/layout-section}}
435 435  {{/layout}}
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1 -235031805
1 +250178591
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1 -https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/250178591/14. Serial Crystallography: CFEL TapeDrive