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

From version 82.1
edited by tabermah
on 2024-12-10 15:22
Change comment: There is no comment for this version
To version 73.1
edited by ahenkel
on 2022-05-07 19:02
Change comment: There is no comment for this version

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Title
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1 -08. Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.tabermah
1 +XWiki.ahenkel
Content
... ... @@ -3,13 +3,15 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 -{{toc/}}
8 +{{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 11  
12 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. Sample characteristics and preparation =
14 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
13 13  
14 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.
15 15  
... ... @@ -19,10 +19,12 @@
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"/}}8.2. Connecting sample to ElveFlow, sample exchange =
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
26 26  
27 27  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!**
28 28  
... ... @@ -38,28 +38,29 @@
38 38  
39 39  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40 40  
45 +\\
41 41  
42 42  ----
43 43  
44 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. TapeDrive operation =
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 +** ==
45 45  
46 -​​​​​​The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
47 -
52 +The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
48 48  Now start the client. Same thing, a terminal will open, shortly after a small window.
49 49  
50 50  Click 'Devices' in the **client session** to open the control window.
51 51  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
52 52  
53 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}Tape ==
58 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
54 54  
55 55  * Click the 'main tape' icon
56 56  * Change the velocity by typing anything from **0.3-3.0 mm/s**
57 57  * Common velocity is 1.0-1.5 mm/s
58 58  * 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.
59 -
64 +\\
60 60  * [[image:attach:kamzik_tape.PNG||height="400"]]
61 61  
62 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
67 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
63 63  
64 64  * Click on the 'nozzle' icon.
65 65  * (((
... ... @@ -67,16 +67,16 @@
67 67  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
68 68  
69 69  
70 -(% 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);" %)** !!!**(%%)
71 71  \\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.
72 72  
73 73  (% class="wrapped" %)
74 74  |=(((
75 -
80 +\\
76 76  )))|=(((
77 77  direction
78 78  )))|=(((
79 -recommended step size
84 +recommended step size
80 80  for visual adjustment
81 81  )))|=(% colspan="1" %)(((
82 82  recommended step size
... ... @@ -111,30 +111,38 @@
111 111  be careful with -z, tape could be pushed out of focus
112 112  )))
113 113  
114 -
119 +**
120 +\\**
115 115  )))
116 116  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
117 117  
118 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
124 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
119 119  
120 120  * The chiller circulates fluid through the gas nozzle.
121 121  
122 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
128 +\\
123 123  
130 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
124 124  
125 -== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
132 +\\
126 126  
134 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
127 127  
136 +\\
137 +
128 128  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
129 129  
130 130   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
131 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
132 132  
144 +\\
133 133  
146 +\\
134 134  
135 135  ----
136 136  
137 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
138 138  
139 139  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).
140 140  
... ... @@ -143,7 +143,7 @@
143 143  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
144 144  * Cut the first cm of the new tape roll, directly behind the black sticky part.
145 145  * 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.
146 -* 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!!!//
147 147  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
148 148  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
149 149  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -150,11 +150,15 @@
150 150  * Close tape stabilizer.
151 151  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
152 152  
153 -**[[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 +**
154 154  
169 +\\
155 155  
171 +\\
156 156  
157 -
173 +**
174 +**
158 158  {{/layout-cell}}
159 159  {{/layout-section}}
160 160  
... ... @@ -162,19 +162,19 @@
162 162  {{layout-cell}}
163 163  ----
164 164  
165 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
166 166  
167 167  start chopper gui from terminal:
168 168  
169 169  (% class="code" %)
170 170  (((
171 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
172 172  )))
173 173  
174 174  (% class="code" %)
175 175  (((
176 176   python chopperControl.py
177 -\\
194 +\\\\
178 178  )))
179 179  {{/layout-cell}}
180 180  {{/layout-section}}
... ... @@ -187,17 +187,18 @@
187 187  {{layout-cell}}
188 188  **Chopper → no Chopper**
189 189  
190 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
191 191  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
192 192  * at frequency = 10 Hz, click "Stop"
193 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
194 194  
195 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
196 196  
197 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
198 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
199 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
200 -* (% 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 +//
201 201  {{/layout-cell}}
202 202  {{/layout-section}}
203 203  
... ... @@ -205,19 +205,19 @@
205 205  {{layout-cell}}
206 206  ----
207 207  
208 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
209 209  
210 210  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
211 211  
212 212  (% class="code" %)
213 213  (((
214 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
232 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
215 215   password: written on control laptop (changes every 6 months)
216 216  )))
217 217  
218 218   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
219 219  
220 -
238 +\\
221 221  {{/layout-cell}}
222 222  {{/layout-section}}
223 223  
... ... @@ -225,26 +225,26 @@
225 225  {{layout-cell}}
226 226  **Check list:**
227 227  
228 -(% style="color:#ff0000" %)//always after entering the hutch!//
246 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
229 229  
230 -(% style="color:#000000" %)Click "Run" icon in kamzik.
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
231 231  
232 -* Put detector distance 200 in //prepare_for_measurement (      )//
233 -* Click "<Call>" next to //prepare_for_measurement//
234 -This will:
235 -** drive the collimator in //IN// position
236 -** drive detector to 200 mm
250 +* Put collimator in
251 +** Put detector distance 200 in //prepare_for_measurement (      )
252 +//
253 +** Click "<Call>" next to //prepare_for_measurement//
237 237  
238 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
255 +\\
239 239  
257 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
258 +
259 +\\
260 +
240 240  //**Set run parameters and go 🏃💥**//
241 241  
242 242  1. Set your desired No. of frames
243 -1. Enter the protein ID of your crystal sample
244 244  1. Match exposure time with chopper setting or set desired exposure time
245 245  1. Check trigger setting and match to chopper setting
246 -no chopper → external triffer //off//
247 - chopper → external trigger// on//
248 248  1. To start the run, click "<Call>" next to //start_run (exposure    )//
249 249  {{/layout-cell}}
250 250  
... ... @@ -255,7 +255,7 @@
255 255  
256 256  {{layout-section ac:type="single"}}
257 257  {{layout-cell}}
258 -(% class="relative-table wrapped" style="width:55.9569%" %)
276 +(% class="relative-table wrapped" %)
259 259  |=(((
260 260  Parameter
261 261  )))|=(((
... ... @@ -266,7 +266,7 @@
266 266  |(((
267 267  Images number
268 268  )))|(((
269 -number of frames you want to collect
287 +Set number of frames you want to collect
270 270  )))|(% colspan="1" %)(((
271 271  usually 100k - 200k, but adjust according to hitrate
272 272  
... ... @@ -277,9 +277,12 @@
277 277  )))|(((
278 278  exposure time of Eiger
279 279  
280 -
298 +\\
281 281  )))|(% colspan="1" %)(((
282 -with chopper         → opening time displayed in chopper GUI
300 +chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
301 +
302 +chopper at 66 Hz   → 7.7 ms
303 +
283 283  no chopper            → 7.7 ms
284 284  
285 285  ----
... ... @@ -289,7 +289,7 @@
289 289  )))|(((
290 290  changes automatically
291 291  )))|(% colspan="1" %)(((
292 -
313 +\\
293 293  )))
294 294  |(% colspan="1" %)(((
295 295  Detector distance
... ... @@ -296,14 +296,14 @@
296 296  )))|(% colspan="1" %)(((
297 297  current detector postion readout
298 298  )))|(% colspan="1" %)(((
299 -
320 +\\
300 300  )))
301 301  |(% colspan="1" %)(((
302 -protein ID
323 +move_detector (distance)
303 303  )))|(% colspan="1" %)(((
304 -protein ID of crystal sample (see AMARCORD)
325 +Set detector distance
305 305  )))|(% colspan="1" %)(((
306 -
327 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
307 307  )))
308 308  
309 309  ----
... ... @@ -324,11 +324,15 @@
324 324  {{/layout-cell}}
325 325  
326 326  {{layout-cell}}
327 -
348 +\\
328 328  
350 +\\
329 329  
352 +\\
330 330  
354 +\\
331 331  
356 +\\
332 332  
333 333  [[image:attach:safety_kamzik.PNG]]
334 334  {{/layout-cell}}
... ... @@ -338,17 +338,19 @@
338 338  {{layout-cell}}
339 339  ----
340 340  
341 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
366 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
342 342  
343 343  * (((
344 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
369 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
345 345  
346 346  * Tape roll empty?
347 347  * motor connected (icon green)?
348 348  )))
349 349  
375 +\\
376 +
350 350  * (((
351 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
378 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
352 352  
353 353  * displayed in green=connected?
354 354  * nozzle holder colliding somewhere?
... ... @@ -355,8 +355,10 @@
355 355  * motor limits reached? → position displayed in red
356 356  )))
357 357  
385 +\\
386 +
358 358  * (((
359 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
388 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
360 360  
361 361  * channel turned on?
362 362  * Sample empty?
... ... @@ -363,21 +363,20 @@
363 363  * Nozzle or lines clogged? → flush with water, change nozzle
364 364  )))
365 365  
395 +\\
396 +
366 366  * (((
367 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
398 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
368 368  
369 369  * First, restart kamzik (server+client) and see if this solves the issue
370 370  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
371 371  * (((
372 -If nothing works, kill the Simplon process and then start the server again:*
373 -
374 -(((
403 +If nothing works, kill the Simplon process and then start the server again:* (((
375 375  (% class="code" %)
376 376  (((
377 377  ssh haspp11exp03
378 378  )))
379 379  )))
380 -
381 381  * (((
382 382  (% class="code" %)
383 383  (((
... ... @@ -391,7 +391,6 @@
391 391  )))
392 392  )))
393 393  )))
394 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
395 395  )))
396 396  {{/layout-cell}}
397 397  {{/layout-section}}
... ... @@ -398,7 +398,7 @@
398 398  
399 399  {{layout-section ac:type="single"}}
400 400  {{layout-cell}}
401 -
428 +\\
402 402  {{/layout-cell}}
403 403  {{/layout-section}}
404 404  {{/layout}}
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1 +254729375
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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/254729375/14. Serial Crystallography: CFEL TapeDrive
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