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Version 74.1 by ahenkel on 2022-05-07 19:08
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ahenkel 37.1 1 {{layout}}
2 {{layout-section ac:type="single"}}
3 {{layout-cell}}
ahenkel 54.1 4 [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
ahenkel 7.1 5
ahenkel 23.1 6 \\
ahenkel 3.1 7
ahenkel 46.1 8 {{toc minLevel="2"/}}
9
ahenkel 23.1 10 \\
11
ahenkel 47.1 12 ----
13
ahenkel 45.1 14 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
ahenkel 23.1 15
ahenkel 55.1 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.
ahenkel 5.1 17
18 Preparation:
19
ahenkel 60.1 20 * filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
ahenkel 5.1 21
ahenkel 12.1 22 [[image:attach:20211201_095534.jpg||height="250"]]
ahenkel 5.1 23
24 \\
25
ahenkel 47.1 26 ----
27
ahenkel 45.1 28 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 ** ==
ahenkel 6.1 30
ahenkel 22.1 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!**
ahenkel 5.1 32
ahenkel 21.1 33 Be aware to which channel and nozzle line your sample is connected.
34
ahenkel 31.1 35 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
ahenkel 21.1 36
ahenkel 22.1 37 Green → Channel 2, substrate line (nozzle capillary is marked in black)
ahenkel 21.1 38
39 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
40
ahenkel 28.1 41 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
ahenkel 5.1 42
ahenkel 28.1 43 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
44
ahenkel 5.1 45 \\
ahenkel 6.1 46
ahenkel 47.1 47 ----
48
ahenkel 45.1 49 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 ** ==
ahenkel 6.1 51
ahenkel 19.1 52 The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
ahenkel 14.1 53 Now start the client. Same thing, a terminal will open, shortly after a small window.
ahenkel 16.1 54
55 Click 'Devices' in the **client session** to open the control window.
ahenkel 15.1 56 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
ahenkel 13.1 57
ahenkel 45.1 58 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
ahenkel 14.1 59
ahenkel 63.1 60 * Click the 'main tape' icon
ahenkel 23.1 61 * Change the velocity by typing anything from **0.3-3.0 mm/s**
62 * Common velocity is 1.0-1.5 mm/s
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.
ahenkel 14.1 64 \\
ahenkel 23.1 65 * [[image:attach:kamzik_tape.PNG||height="400"]]
ahenkel 14.1 66
ahenkel 26.1 67 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
ahenkel 23.1 68
ahenkel 62.1 69 * Click on the 'nozzle' icon.
ahenkel 23.1 70 * (((
ahenkel 19.1 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.
ahenkel 17.1 72 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
73
ahenkel 36.1 74
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 \\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
ahenkel 44.1 78 (% class="wrapped" %)
ahenkel 17.1 79 |=(((
ahenkel 14.1 80 \\
ahenkel 17.1 81 )))|=(((
82 direction
83 )))|=(((
84 recommended step size
85 for visual adjustment
86 )))|=(% colspan="1" %)(((
87 recommended step size
88 during data collection
89 )))
90 |(((
91 +x
92 )))|(((
ahenkel 18.1 93 away from X-ray interaction point
ahenkel 17.1 94 )))|(((
95 1.0 - 0.5 mm
96 )))|(% colspan="1" %)(((
97 0.1 - 0.2 mm
98 )))
99 |(((
100 +y
101 )))|(((
102 up
103 )))|(((
104 1.0 - 0.5 mm
105 )))|(% colspan="1" %)(((
106 0.1 - 0.2 mm
107 )))
108 |(((
109 +z
110 )))|(((
111 towards detector tower, away from tape
112 )))|(((
113 0.5 - 0.2 mm
114 )))|(% colspan="1" %)(((
115 0.1 - 0.2 mm
116 be careful with -z, tape could be pushed out of focus
117 )))
ahenkel 14.1 118
ahenkel 19.1 119 **
ahenkel 17.1 120 \\**
121 )))
ahenkel 23.1 122 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
ahenkel 17.1 123
ahenkel 23.1 124 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
125
ahenkel 34.1 126 * The chiller circulates fluid through the gas nozzle.
ahenkel 30.1 127
ahenkel 14.1 128 \\
129
ahenkel 32.1 130 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
ahenkel 17.1 131
132 \\
133
ahenkel 33.1 134 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
135
ahenkel 23.1 136 \\
137
ahenkel 13.1 138 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
139
140 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
141 password: //written on control laptop (changes every 6 months)
142 //
143
ahenkel 6.1 144 \\
145
ahenkel 7.1 146 \\
ahenkel 6.1 147
ahenkel 47.1 148 ----
ahenkel 12.1 149
ahenkel 47.1 150 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151
ahenkel 19.1 152 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).
ahenkel 12.1 153
ahenkel 19.1 154 * Remove the (almost) empty feeder roll by pulling it upwards.
ahenkel 22.1 155 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
ahenkel 19.1 156 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
ahenkel 35.1 157 * Cut the first cm of the new tape roll, directly behind the black sticky part.
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.
ahenkel 56.1 159 * Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
ahenkel 35.1 160 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
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 * Attach new tape to the empty roll by using some sticky tape.
ahenkel 22.1 163 * Close tape stabilizer.
ahenkel 35.1 164 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
ahenkel 19.1 165
ahenkel 36.1 166 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
ahenkel 19.1 167 **
168
ahenkel 6.1 169 \\
170
171 \\
ahenkel 7.1 172
ahenkel 48.1 173 **
174 **
ahenkel 43.1 175 {{/layout-cell}}
176 {{/layout-section}}
ahenkel 28.1 177
ahenkel 43.1 178 {{layout-section ac:type="single"}}
179 {{layout-cell}}
ahenkel 47.1 180 ----
ahenkel 12.1 181
ahenkel 47.1 182 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183
ahenkel 42.1 184 start chopper gui from terminal:
ahenkel 28.1 185
ahenkel 42.1 186 (% class="code" %)
187 (((
188 cd /gpfs/local/shared/ChopperControl
189 )))
190
191 (% class="code" %)
192 (((
193 python chopperControl.py
ahenkel 47.1 194 \\\\
ahenkel 42.1 195 )))
196 {{/layout-cell}}
197 {{/layout-section}}
198
199 {{layout-section ac:type="two_equal"}}
200 {{layout-cell}}
201 [[image:attach:20211212_233140.jpg||height="250"]]
202 {{/layout-cell}}
203
204 {{layout-cell}}
205 **Chopper → no Chopper**
206
207 * decrease frequency by max. 10 Hz steps\\
208 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
209 * at frequency = 10 Hz, click "Stop"
210 * set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
211
212 (% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
213
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", .....
ahenkel 65.1 217 * (% 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 //
ahenkel 42.1 219 {{/layout-cell}}
220 {{/layout-section}}
221
ahenkel 59.1 222 {{layout-section ac:type="single"}}
ahenkel 42.1 223 {{layout-cell}}
ahenkel 69.1 224 ----
225
ahenkel 47.1 226 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227
ahenkel 36.1 228 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
229
ahenkel 40.1 230 (% class="code" %)
231 (((
232 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
233 password: written on control laptop (changes every 6 months)
234 )))
ahenkel 36.1 235
ahenkel 51.1 236 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
ahenkel 36.1 237
ahenkel 12.1 238 \\
ahenkel 59.1 239 {{/layout-cell}}
240 {{/layout-section}}
ahenkel 12.1 241
ahenkel 59.1 242 {{layout-section ac:type="two_left_sidebar"}}
243 {{layout-cell}}
ahenkel 51.1 244 **Check list:**
ahenkel 40.1 245
ahenkel 51.1 246 (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
ahenkel 40.1 247
ahenkel 67.1 248 (% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
ahenkel 51.1 249
250 * Put collimator in
ahenkel 67.1 251 ** Put detector distance 200 in //prepare_for_measurement (      )
252 //
253 ** Click "<Call>" next to //prepare_for_measurement//
ahenkel 51.1 254
255 \\
256
ahenkel 59.1 257 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
ahenkel 51.1 258
ahenkel 68.1 259 \\
ahenkel 40.1 260
ahenkel 68.1 261 //**Set run parameters and go 🏃💥**//
ahenkel 36.1 262
ahenkel 39.1 263 1. Set your desired No. of frames
ahenkel 67.1 264 1. Match exposure time with chopper setting or set desired exposure time
ahenkel 39.1 265 1. Check trigger setting and match to chopper setting
ahenkel 74.1 266 no chopper → external triffer //off
267 // chopper → external trigger// on
268 //
ahenkel 68.1 269 1. To start the run, click "<Call>" next to //start_run (exposure    )//
270 {{/layout-cell}}
ahenkel 40.1 271
ahenkel 68.1 272 {{layout-cell}}
ahenkel 69.1 273 [[image:attach:Kamzik_run(2).PNG]]
ahenkel 37.1 274 {{/layout-cell}}
ahenkel 68.1 275 {{/layout-section}}
ahenkel 37.1 276
ahenkel 71.1 277 {{layout-section ac:type="single"}}
ahenkel 37.1 278 {{layout-cell}}
ahenkel 74.1 279 (% class="relative-table wrapped" style="width: 55.9569%;" %)
ahenkel 36.1 280 |=(((
281 Parameter
282 )))|=(((
283 explanation
284 )))|=(% colspan="1" %)(((
285 value
286 )))
287 |(((
288 Images number
289 )))|(((
ahenkel 74.1 290 number of frames you want to collect
ahenkel 36.1 291 )))|(% colspan="1" %)(((
292 usually 100k - 200k, but adjust according to hitrate
293
294 orientation: 10 % hitrate needs at least 100k images
295 )))
296 |(((
297 exposure
298 )))|(((
299 exposure time of Eiger
300
301 \\
302 )))|(% colspan="1" %)(((
ahenkel 65.1 303 chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
ahenkel 36.1 304
305 chopper at 66 Hz   → 7.7 ms
306
307 no chopper            → 7.7 ms
308
309 ----
310 )))
311 |(((
312 run id
313 )))|(((
314 changes automatically
315 )))|(% colspan="1" %)(((
316 \\
317 )))
318 |(% colspan="1" %)(((
319 Detector distance
320 )))|(% colspan="1" %)(((
321 current detector postion readout
322 )))|(% colspan="1" %)(((
323 \\
324 )))
ahenkel 68.1 325
ahenkel 71.1 326 ----
ahenkel 69.1 327 {{/layout-cell}}
328 {{/layout-section}}
329
330 {{layout-section ac:type="two_equal"}}
331 {{layout-cell}}
ahenkel 68.1 332 **After data collection/Before entering the exp. hutch:**
333
334 1. Go to "Safety" in kamzik.
335 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
336 11. Drive the collimator out
337 11. Drive the detector back to 1500 mm
338 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
339
ahenkel 70.1 340 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
ahenkel 68.1 341 {{/layout-cell}}
ahenkel 69.1 342
343 {{layout-cell}}
ahenkel 72.1 344 \\
345
346 \\
347
348 \\
349
350 \\
351
352 \\
353
ahenkel 69.1 354 [[image:attach:safety_kamzik.PNG]]
355 {{/layout-cell}}
ahenkel 37.1 356 {{/layout-section}}
ahenkel 36.1 357
ahenkel 37.1 358 {{layout-section ac:type="single"}}
359 {{layout-cell}}
ahenkel 41.1 360 ----
361
ahenkel 47.1 362 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
ahenkel 29.1 363
364 * (((
365 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
ahenkel 41.1 366
367 * Tape roll empty?
368 * motor connected (icon green)?
ahenkel 29.1 369 )))
ahenkel 41.1 370
371 \\
372
ahenkel 29.1 373 * (((
374 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
ahenkel 41.1 375
376 * displayed in green=connected?
377 * nozzle holder colliding somewhere?
378 * motor limits reached? → position displayed in red
ahenkel 29.1 379 )))
ahenkel 41.1 380
381 \\
382
ahenkel 29.1 383 * (((
384 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
ahenkel 41.1 385
386 * channel turned on?
387 * Sample empty?
388 * Nozzle or lines clogged? → flush with water, change nozzle
ahenkel 29.1 389 )))
ahenkel 51.1 390
391 \\
392
ahenkel 49.1 393 * (((
394 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
395
396 * First, restart kamzik (server+client) and see if this solves the issue
397 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
ahenkel 51.1 398 * (((
399 If nothing works, kill the Simplon process and then start the server again:* (((
400 (% class="code" %)
401 (((
402 ssh haspp11exp03
ahenkel 49.1 403 )))
ahenkel 51.1 404 )))
405 * (((
406 (% class="code" %)
407 (((
408 ps -ef | grep Simplon
409 )))
410 )))
411 * (((
412 (% class="code" %)
413 (((
414 kill -9 simplon_process_id
415 )))
416 )))
417 )))
418 )))
ahenkel 37.1 419 {{/layout-cell}}
420 {{/layout-section}}
ahenkel 51.1 421
422 {{layout-section ac:type="single"}}
423 {{layout-cell}}
424 \\
425 {{/layout-cell}}
426 {{/layout-section}}
ahenkel 37.1 427 {{/layout}}