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Last modified by chatzies on 2025-11-27 11:35
From version 77.1
edited by tabermah
on 2024-12-03 11:26
Change comment: There is no comment for this version
To version 66.1
edited by ahenkel
on 2022-05-06 17:27
Change comment: There is no comment for this version

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Title
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1 -10. Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.tabermah
1 +XWiki.ahenkel
Content
... ... @@ -3,9 +3,11 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 7  {{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 11  
... ... @@ -19,12 +19,11 @@
19 19  
20 20  [[image:attach:20211201_095534.jpg||height="250"]]
21 21  
24 +\\
22 22  
23 23  ----
24 24  
25 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26 -
27 -*
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
28 28  ** ==
29 29  
30 30  After filtration, screw the ElveFlow connector to your Eppendorf or Falcon tube. Make sure that the yellow-ish line goes to the bottom of your tube. You can adjust the length by unscrewing the blue fitting on top and pushing/pulling the yellow-ish line. **Don't forget to tigthen the blue fitting afterwards!**
... ... @@ -41,15 +41,14 @@
41 41  
42 42  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
43 43  
45 +\\
44 44  
45 45  ----
46 46  
47 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48 -
49 -*
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 50  ** ==
51 51  
52 -The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
52 +The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
53 53  Now start the client. Same thing, a terminal will open, shortly after a small window.
54 54  
55 55  Click 'Devices' in the **client session** to open the control window.
... ... @@ -61,7 +61,7 @@
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.
64 -
64 +\\
65 65  * [[image:attach:kamzik_tape.PNG||height="400"]]
66 66  
67 67  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
... ... @@ -72,16 +72,16 @@
72 72  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
73 73  
74 74  
75 -(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
75 +(% style="color: rgb(255,0,0);" %)**!!! **(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color: rgb(255,0,0);" %)** !!!**(%%)
76 76  \\Adjust the nozzle position by eye until it nearly touches the tape and roughly meets the X-ray interaction point. Then, move to the control hutch to use the on-axis microscope for fine adjustment. Move the nozzle tip to the beam position (red X) and write down the absolut nozzle position. From there move the nozzle in +x to your desired distance.Different distances combined with the tape speed result in several delay times for time-resolved experiments.
77 77  
78 78  (% class="wrapped" %)
79 79  |=(((
80 -
80 +\\
81 81  )))|=(((
82 82  direction
83 83  )))|=(((
84 -recommended step size
84 +recommended step size
85 85  for visual adjustment
86 86  )))|=(% colspan="1" %)(((
87 87  recommended step size
... ... @@ -116,8 +116,8 @@
116 116  be careful with -z, tape could be pushed out of focus
117 117  )))
118 118  
119 -
120 -
119 +**
120 +\\**
121 121  )))
122 122  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
123 123  
... ... @@ -125,19 +125,25 @@
125 125  
126 126  * The chiller circulates fluid through the gas nozzle.
127 127  
128 +\\
128 128  
129 129  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
130 130  
132 +\\
131 131  
132 132  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
133 133  
136 +\\
134 134  
135 135  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
136 136  
137 137   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
138 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
139 139  
144 +\\
140 140  
146 +\\
141 141  
142 142  ----
143 143  
... ... @@ -150,7 +150,7 @@
150 150  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
151 151  * Cut the first cm of the new tape roll, directly behind the black sticky part.
152 152  * 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.
153 -* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
154 154  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
155 155  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
156 156  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -157,11 +157,15 @@
157 157  * Close tape stabilizer.
158 158  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
159 159  
160 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
166 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 +**
161 161  
169 +\\
162 162  
171 +\\
163 163  
164 -
173 +**
174 +**
165 165  {{/layout-cell}}
166 166  {{/layout-section}}
167 167  
... ... @@ -175,13 +175,13 @@
175 175  
176 176  (% class="code" %)
177 177  (((
178 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
179 179  )))
180 180  
181 181  (% class="code" %)
182 182  (((
183 183   python chopperControl.py
184 -\\
194 +\\\\
185 185  )))
186 186  {{/layout-cell}}
187 187  {{/layout-section}}
... ... @@ -194,24 +194,23 @@
194 194  {{layout-cell}}
195 195  **Chopper → no Chopper**
196 196  
197 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
198 198  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
199 199  * at frequency = 10 Hz, click "Stop"
200 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
201 201  
202 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
203 203  
204 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
205 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
206 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
207 -* (% style="color:#000000" %)//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//
214 +* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
215 +* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
216 +** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
217 +* (% 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
218 +//
208 208  {{/layout-cell}}
209 209  {{/layout-section}}
210 210  
211 211  {{layout-section ac:type="single"}}
212 212  {{layout-cell}}
213 -----
214 -
215 215  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
216 216  
217 217  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
... ... @@ -218,13 +218,13 @@
218 218  
219 219  (% class="code" %)
220 220  (((
221 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
230 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
222 222   password: written on control laptop (changes every 6 months)
223 223  )))
224 224  
225 225   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
226 226  
227 -
236 +\\
228 228  {{/layout-cell}}
229 229  {{/layout-section}}
230 230  
... ... @@ -232,39 +232,62 @@
232 232  {{layout-cell}}
233 233  **Check list:**
234 234  
235 -(% style="color:#ff0000" %)//always after entering the hutch!//
244 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
236 236  
237 -(% style="color:#000000" %)Click "Run" icon in kamzik.
246 +(% style="color: rgb(0,0,0);" %)Click "Safety" icon in kamzik.
238 238  
239 -* Put detector distance 200 in //prepare_for_measurement (      )//
240 -* Click "<Call>" next to //prepare_for_measurement//
241 -This will:
242 -** drive the collimator in //IN// position
243 -** drive detector to 200 mm
248 +* Put collimator in
249 +** Click "<Call>" next to //collimator_in//
244 244  
251 +\\
245 245  
246 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
253 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
254 +{{/layout-cell}}
247 247  
256 +{{layout-cell}}
257 +[[image:attach:kamzik_safety.PNG||height="400"]]
258 +{{/layout-cell}}
259 +{{/layout-section}}
248 248  
249 -//**Set run parameters and go 🏃💥**//
261 +{{layout-section ac:type="single"}}
262 +{{layout-cell}}
263 +----
250 250  
251 -1. Set your desired No. of frames
252 -1. Enter the protein ID of your crystal sample
253 -1. Match exposure time with chopper setting or set desired exposure time
254 -1. Check trigger setting and match to chopper setting
255 -no chopper → external triffer //off//
256 - chopper → external trigger// on//
257 -1. To start the run, click "<Call>" next to //start_run (exposure    )//
265 +Click "Start/Run" icon in kamzik.
266 +
267 +[[image:attach:kamzik_run-tile.jpg||height="400"]]
268 +
269 +----
258 258  {{/layout-cell}}
271 +{{/layout-section}}
259 259  
273 +{{layout-section ac:type="two_equal"}}
260 260  {{layout-cell}}
261 -[[image:attach:Kamzik_run(2).PNG]]
275 +**Set run parameters and go 🏃💥**
276 +
277 +1. Set your desired No. of frames
278 +1. Match exposure time with chopper setting
279 +1. Check trigger setting and match to chopper setting
280 +1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
281 +1. To start the run, click "<Call>" next to //exposure time//
282 +
283 +\\
284 +
285 +\\
286 +
287 +**After data collection/Before entering the exp. hutch:**
288 +
289 +1. Go to "Safety" in kamzik.
290 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
291 +11. Drive the collimator out
292 +11. Drive the detector back to 1500 mm
293 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
294 +
295 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
262 262  {{/layout-cell}}
263 -{{/layout-section}}
264 264  
265 -{{layout-section ac:type="single"}}
266 266  {{layout-cell}}
267 -(% class="relative-table wrapped" style="width:55.9569%" %)
299 +(% class="wrapped relative-table" style="width: 100.0%;" %)
268 268  |=(((
269 269  Parameter
270 270  )))|=(((
... ... @@ -275,7 +275,7 @@
275 275  |(((
276 276  Images number
277 277  )))|(((
278 -number of frames you want to collect
310 +Set number of frames you want to collect
279 279  )))|(% colspan="1" %)(((
280 280  usually 100k - 200k, but adjust according to hitrate
281 281  
... ... @@ -286,9 +286,12 @@
286 286  )))|(((
287 287  exposure time of Eiger
288 288  
289 -
321 +\\
290 290  )))|(% colspan="1" %)(((
291 -with chopper         → opening time displayed in chopper GUI
323 +chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
324 +
325 +chopper at 66 Hz   → 7.7 ms
326 +
292 292  no chopper            → 7.7 ms
293 293  
294 294  ----
... ... @@ -298,7 +298,7 @@
298 298  )))|(((
299 299  changes automatically
300 300  )))|(% colspan="1" %)(((
301 -
336 +\\
302 302  )))
303 303  |(% colspan="1" %)(((
304 304  Detector distance
... ... @@ -305,44 +305,18 @@
305 305  )))|(% colspan="1" %)(((
306 306  current detector postion readout
307 307  )))|(% colspan="1" %)(((
308 -
343 +\\
309 309  )))
310 310  |(% colspan="1" %)(((
311 -protein ID
346 +move_detector (distance)
312 312  )))|(% colspan="1" %)(((
313 -protein ID of crystal sample (see AMARCORD)
348 +Set detector distance
314 314  )))|(% colspan="1" %)(((
315 -
350 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
316 316  )))
317 -
318 -----
319 319  {{/layout-cell}}
320 320  {{/layout-section}}
321 321  
322 -{{layout-section ac:type="two_equal"}}
323 -{{layout-cell}}
324 -**After data collection/Before entering the exp. hutch:**
325 -
326 -1. Go to "Safety" in kamzik.
327 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
328 -11. Drive the collimator out
329 -11. Drive the detector back to 1500 mm
330 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
331 -
332 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
333 -{{/layout-cell}}
334 -
335 -{{layout-cell}}
336 -
337 -
338 -
339 -
340 -
341 -
342 -[[image:attach:safety_kamzik.PNG]]
343 -{{/layout-cell}}
344 -{{/layout-section}}
345 -
346 346  {{layout-section ac:type="single"}}
347 347  {{layout-cell}}
348 348  ----
... ... @@ -356,6 +356,7 @@
356 356  * motor connected (icon green)?
357 357  )))
358 358  
368 +\\
359 359  
360 360  * (((
361 361  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
... ... @@ -365,6 +365,7 @@
365 365  * motor limits reached? → position displayed in red
366 366  )))
367 367  
378 +\\
368 368  
369 369  * (((
370 370  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
... ... @@ -374,6 +374,7 @@
374 374  * Nozzle or lines clogged? → flush with water, change nozzle
375 375  )))
376 376  
388 +\\
377 377  
378 378  * (((
379 379  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
... ... @@ -381,15 +381,12 @@
381 381  * First, restart kamzik (server+client) and see if this solves the issue
382 382  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
383 383  * (((
384 -If nothing works, kill the Simplon process and then start the server again:*
385 -
386 -(((
396 +If nothing works, kill the Simplon process and then start the server again:* (((
387 387  (% class="code" %)
388 388  (((
389 389  ssh haspp11exp03
390 390  )))
391 391  )))
392 -
393 393  * (((
394 394  (% class="code" %)
395 395  (((
... ... @@ -403,7 +403,6 @@
403 403  )))
404 404  )))
405 405  )))
406 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
407 407  )))
408 408  {{/layout-cell}}
409 409  {{/layout-section}}
... ... @@ -410,7 +410,7 @@
410 410  
411 411  {{layout-section ac:type="single"}}
412 412  {{layout-cell}}
413 -
421 +\\
414 414  {{/layout-cell}}
415 415  {{/layout-section}}
416 416  {{/layout}}
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1 -235031805
1 +254729365
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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/254729365/14. Serial Crystallography: CFEL TapeDrive