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Last modified by chatzies on 2025-11-27 11:35
From version 84.1
edited by tabermah
on 2024-12-10 15:55
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To version 60.1
edited by ahenkel
on 2022-04-14 11:58
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
... ... @@ -3,28 +3,32 @@
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 -* 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 (green) or 50 µm (yellow) cell filter into an 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  
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 -After filtration, screw the ElveFlow connector to your Eppendorf or Falcon tube. Make sure that the yellow-ish tube goes all the way 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!**
31 +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  
29 29  Be aware to which channel and nozzle line your sample is connected.
30 30  
... ... @@ -38,47 +38,46 @@
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 -* Click the 'main tape' icon
60 +* Click on 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 +\\
65 +* [[image:attach:kamzik_tape.PNG||height="400"]]
60 60  
61 -[[image:attach:kamzik_tape.PNG||height="400"]]
67 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
62 62  
63 -
64 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
65 -
66 -* Click on the 'nozzle' icon.
69 +* Click an the 'nozzle' icon.
67 67  * (((
68 68  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.
69 69  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
70 70  
71 71  
72 -(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving the nozzle, 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);" %)** !!!**(%%)
73 73  \\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.
74 74  
75 75  (% class="wrapped" %)
76 76  |=(((
77 -
80 +\\
78 78  )))|=(((
79 79  direction
80 80  )))|=(((
81 -recommended step size
84 +recommended step size
82 82  for visual adjustment
83 83  )))|=(% colspan="1" %)(((
84 84  recommended step size
... ... @@ -113,32 +113,38 @@
113 113  be careful with -z, tape could be pushed out of focus
114 114  )))
115 115  
116 -
119 +**
120 +\\**
117 117  )))
122 +* [[image:attach:kamzik_nozzle.PNG||height="400"]]
118 118  
119 -[[image:attach:kamzik_nozzle.PNG||height="400"]]
124 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
120 120  
121 -
122 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
123 -
124 124  * The chiller circulates fluid through the gas nozzle.
125 125  
126 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
128 +\\
127 127  
130 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
128 128  
129 -== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
132 +\\
130 130  
134 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
131 131  
136 +\\
137 +
132 132  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
133 133  
134 134   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
135 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
136 136  
144 +\\
137 137  
146 +\\
138 138  
139 139  ----
140 140  
141 -= {{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** ==
142 142  
143 143  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).
144 144  
... ... @@ -147,7 +147,7 @@
147 147  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
148 148  * Cut the first cm of the new tape roll, directly behind the black sticky part.
149 149  * 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.
150 -* 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!!!//
151 151  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
152 152  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
153 153  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -154,9 +154,15 @@
154 154  * Close tape stabilizer.
155 155  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
156 156  
157 -**[[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 +**
158 158  
159 -
169 +\\
170 +
171 +\\
172 +
173 +**
174 +**
160 160  {{/layout-cell}}
161 161  {{/layout-section}}
162 162  
... ... @@ -164,19 +164,19 @@
164 164  {{layout-cell}}
165 165  ----
166 166  
167 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
168 168  
169 169  start chopper gui from terminal:
170 170  
171 171  (% class="code" %)
172 172  (((
173 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
174 174  )))
175 175  
176 176  (% class="code" %)
177 177  (((
178 178   python chopperControl.py
179 -\\
194 +\\\\
180 180  )))
181 181  {{/layout-cell}}
182 182  {{/layout-section}}
... ... @@ -189,37 +189,35 @@
189 189  {{layout-cell}}
190 190  **Chopper → no Chopper**
191 191  
192 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
193 193  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
194 194  * at frequency = 10 Hz, click "Stop"
195 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
196 196  
197 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
198 198  
199 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
200 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
201 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
202 -* (% 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//
203 203  {{/layout-cell}}
204 204  {{/layout-section}}
205 205  
206 206  {{layout-section ac:type="single"}}
207 207  {{layout-cell}}
208 -----
223 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
209 209  
210 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
211 -
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-tapetop
229 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
217 217   password: written on control laptop (changes every 6 months)
218 218  )))
219 219  
220 220   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
221 221  
222 -
235 +\\
223 223  {{/layout-cell}}
224 224  {{/layout-section}}
225 225  
... ... @@ -227,37 +227,62 @@
227 227  {{layout-cell}}
228 228  **Check list:**
229 229  
230 -(% style="color:#ff0000" %)//always after entering the hutch!//
243 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
231 231  
232 -(% style="color:#000000" %)Click "Run" icon in kamzik.
245 +(% style="color: rgb(0,0,0);" %)Click "Safety" icon in kamzik.
233 233  
234 -* Put detector distance 200 mm in //prepare_for_measurement (      )//
235 -* Click "<Call>" next to //prepare_for_measurement//
236 -This will:
237 -** drive the collimator in //IN// position
238 -** drive detector to 200 mm
247 +* Put collimator in
248 +** Click "<Call>" next to //collimator_in//
239 239  
240 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
250 +\\
241 241  
242 -//**Set run parameters and go 🏃💥**//
243 -
244 -1. Set your desired No. of frames
245 -1. Enter the protein ID of your crystal sample
246 -1. Match exposure time with chopper setting or set desired exposure time
247 -1. Check trigger setting and match to chopper setting
248 -no chopper → external triffer //off//
249 - chopper → external trigger// on//
250 -1. To start the run, click "<Call>" next to //start_run (exposure    )//
252 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
251 251  {{/layout-cell}}
252 252  
253 253  {{layout-cell}}
254 -[[image:attach:Kamzik_run(2).PNG]]
256 +[[image:attach:kamzik_safety.PNG||height="400"]]
255 255  {{/layout-cell}}
256 256  {{/layout-section}}
257 257  
258 258  {{layout-section ac:type="single"}}
259 259  {{layout-cell}}
260 -(% class="relative-table wrapped" style="width:55.9569%" %)
262 +----
263 +
264 +Click "Start/Run" icon in kamzik.
265 +
266 +[[image:attach:kamzik_run-tile.jpg||height="400"]]
267 +
268 +----
269 +{{/layout-cell}}
270 +{{/layout-section}}
271 +
272 +{{layout-section ac:type="two_equal"}}
273 +{{layout-cell}}
274 +**Set run parameters and go 🏃💥**
275 +
276 +1. Set your desired No. of frames
277 +1. Match exposure time with chopper setting
278 +1. Check trigger setting and match to chopper setting
279 +1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
280 +1. To start the run, click "<Call>" next to //exposure time//
281 +
282 +\\
283 +
284 +\\
285 +
286 +**After data collection/Before entering the exp. hutch:**
287 +
288 +1. Go to "Safety" in kamzik.
289 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
290 +11. Drive the collimator out
291 +11. Drive the detector back to 1500 mm
292 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
293 +
294 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
295 +{{/layout-cell}}
296 +
297 +{{layout-cell}}
298 +(% class="wrapped relative-table" style="width: 100.0%;" %)
261 261  |=(((
262 262  Parameter
263 263  )))|=(((
... ... @@ -268,7 +268,7 @@
268 268  |(((
269 269  Images number
270 270  )))|(((
271 -number of frames you want to collect
309 +Set number of frames you want to collect
272 272  )))|(% colspan="1" %)(((
273 273  usually 100k - 200k, but adjust according to hitrate
274 274  
... ... @@ -279,9 +279,12 @@
279 279  )))|(((
280 280  exposure time of Eiger
281 281  
282 -
320 +\\
283 283  )))|(% colspan="1" %)(((
284 -with chopper         → opening time displayed in chopper GUI
322 +chopper at 133 Hz → 3.7 ms
323 +
324 +chopper at 66 Hz   → 7.7 ms
325 +
285 285  no chopper            → 7.7 ms
286 286  
287 287  ----
... ... @@ -291,7 +291,7 @@
291 291  )))|(((
292 292  changes automatically
293 293  )))|(% colspan="1" %)(((
294 -
335 +\\
295 295  )))
296 296  |(% colspan="1" %)(((
297 297  Detector distance
... ... @@ -298,55 +298,44 @@
298 298  )))|(% colspan="1" %)(((
299 299  current detector postion readout
300 300  )))|(% colspan="1" %)(((
301 -
342 +\\
302 302  )))
303 303  |(% colspan="1" %)(((
304 -protein ID
345 +move_detector (distance)
305 305  )))|(% colspan="1" %)(((
306 -protein ID of crystal sample (see AMARCORD)
347 +Set detector distance
307 307  )))|(% colspan="1" %)(((
308 -
349 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
309 309  )))
310 -
311 -----
351 +|(% colspan="1" %)(((
352 +Diode voltage
353 +)))|(% colspan="1" %)(((
354 +read out of diode
355 +)))|(% colspan="1" %)(((
356 +**~~ 0 !!! higher values indicate missaligned beam stop!!! 
357 +Call local contact
358 +**
359 +)))
312 312  {{/layout-cell}}
313 313  {{/layout-section}}
314 314  
315 -{{layout-section ac:type="two_equal"}}
316 -{{layout-cell}}
317 -**After data collection/Before entering the exp. hutch:**
318 -
319 -1. Go to "Safety" in kamzik.
320 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
321 -11. Drive the collimator out
322 -11. Drive the detector back to 1500 mm
323 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
324 -
325 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
326 -{{/layout-cell}}
327 -
328 -{{layout-cell}}
329 -
330 -
331 -[[image:attach:safety_kamzik.PNG]]
332 -{{/layout-cell}}
333 -{{/layout-section}}
334 -
335 335  {{layout-section ac:type="single"}}
336 336  {{layout-cell}}
337 337  ----
338 338  
339 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
367 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
340 340  
341 341  * (((
342 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
370 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
343 343  
344 344  * Tape roll empty?
345 345  * motor connected (icon green)?
346 346  )))
347 347  
376 +\\
377 +
348 348  * (((
349 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
379 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
350 350  
351 351  * displayed in green=connected?
352 352  * nozzle holder colliding somewhere?
... ... @@ -353,8 +353,10 @@
353 353  * motor limits reached? → position displayed in red
354 354  )))
355 355  
386 +\\
387 +
356 356  * (((
357 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
389 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
358 358  
359 359  * channel turned on?
360 360  * Sample empty?
... ... @@ -361,21 +361,20 @@
361 361  * Nozzle or lines clogged? → flush with water, change nozzle
362 362  )))
363 363  
396 +\\
397 +
364 364  * (((
365 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
399 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
366 366  
367 367  * First, restart kamzik (server+client) and see if this solves the issue
368 368  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
369 369  * (((
370 -If nothing works, kill the Simplon process and then start the server again:*
371 -
372 -(((
404 +If nothing works, kill the Simplon process and then start the server again:* (((
373 373  (% class="code" %)
374 374  (((
375 375  ssh haspp11exp03
376 376  )))
377 377  )))
378 -
379 379  * (((
380 380  (% class="code" %)
381 381  (((
... ... @@ -389,8 +389,13 @@
389 389  )))
390 390  )))
391 391  )))
392 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
393 393  )))
394 394  {{/layout-cell}}
395 395  {{/layout-section}}
426 +
427 +{{layout-section ac:type="single"}}
428 +{{layout-cell}}
429 +\\
430 +{{/layout-cell}}
431 +{{/layout-section}}
396 396  {{/layout}}
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