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Version 80.1 by tabermah on 2024-12-10 15:20
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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 3.1 6
tabermah 79.5 7 {{toc/}}
ahenkel 46.1 8
ahenkel 23.1 9
ahenkel 47.1 10 ----
11
tabermah 79.5 12 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1 Sample characteristics and preparation =
ahenkel 23.1 13
ahenkel 55.1 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.
ahenkel 5.1 15
16 Preparation:
17
ahenkel 60.1 18 * filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
ahenkel 5.1 19
ahenkel 12.1 20 [[image:attach:20211201_095534.jpg||height="250"]]
ahenkel 5.1 21
22
ahenkel 47.1 23 ----
24
tabermah 79.5 25 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}8.2 Connecting sample to ElveFlow, sample exchange =
tabermah 77.1 26
tabermah 79.1 27 *
ahenkel 45.1 28 ** ==
ahenkel 6.1 29
ahenkel 22.1 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!**
ahenkel 5.1 31
ahenkel 21.1 32 Be aware to which channel and nozzle line your sample is connected.
33
ahenkel 31.1 34 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
ahenkel 21.1 35
ahenkel 22.1 36 Green → Channel 2, substrate line (nozzle capillary is marked in black)
ahenkel 21.1 37
38 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
39
ahenkel 28.1 40 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
ahenkel 5.1 41
ahenkel 28.1 42 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
43
ahenkel 6.1 44
ahenkel 47.1 45 ----
46
tabermah 79.5 47 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3 TapeDrive operation =
tabermah 77.1 48
tabermah 79.1 49 *
ahenkel 45.1 50 ** ==
ahenkel 6.1 51
tabermah 77.1 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
tabermah 79.5 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.
tabermah 77.1 64
ahenkel 23.1 65 * [[image:attach:kamzik_tape.PNG||height="400"]]
ahenkel 14.1 66
tabermah 79.5 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
tabermah 77.1 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" %)** !!!**(%%)
ahenkel 36.1 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 |=(((
tabermah 77.1 80
ahenkel 17.1 81 )))|=(((
82 direction
83 )))|=(((
tabermah 77.1 84 recommended step size
ahenkel 17.1 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
tabermah 77.1 119
ahenkel 17.1 120 )))
ahenkel 23.1 121 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
ahenkel 17.1 122
tabermah 79.5 123 == {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
ahenkel 23.1 124
ahenkel 34.1 125 * The chiller circulates fluid through the gas nozzle.
ahenkel 30.1 126
tabermah 79.5 127 == {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
ahenkel 17.1 128
129
tabermah 79.6 130 == {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
ahenkel 33.1 131
ahenkel 23.1 132
ahenkel 13.1 133 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
134
135 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
tabermah 77.1 136 password: //written on control laptop (changes every 6 months)//
ahenkel 13.1 137
ahenkel 6.1 138
139
ahenkel 47.1 140 ----
ahenkel 12.1 141
tabermah 79.6 142 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4 Tape roll exchange =
ahenkel 47.1 143
ahenkel 19.1 144 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 12.1 145
ahenkel 19.1 146 * Remove the (almost) empty feeder roll by pulling it upwards.
ahenkel 22.1 147 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
ahenkel 19.1 148 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
ahenkel 35.1 149 * Cut the first cm of the new tape roll, directly behind the black sticky part.
150 * 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.
tabermah 77.1 151 * Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
ahenkel 35.1 152 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
153 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
154 * Attach new tape to the empty roll by using some sticky tape.
ahenkel 22.1 155 * Close tape stabilizer.
ahenkel 35.1 156 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
ahenkel 19.1 157
tabermah 77.1 158 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
ahenkel 19.1 159
ahenkel 6.1 160
ahenkel 7.1 161
tabermah 77.1 162
ahenkel 43.1 163 {{/layout-cell}}
164 {{/layout-section}}
ahenkel 28.1 165
ahenkel 43.1 166 {{layout-section ac:type="single"}}
167 {{layout-cell}}
ahenkel 47.1 168 ----
ahenkel 12.1 169
tabermah 79.6 170 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5 Chopper =
ahenkel 47.1 171
ahenkel 42.1 172 start chopper gui from terminal:
ahenkel 28.1 173
ahenkel 42.1 174 (% class="code" %)
175 (((
tabermah 77.1 176 cd /gpfs/local/shared/ChopperControl          
ahenkel 42.1 177 )))
178
179 (% class="code" %)
180 (((
181 python chopperControl.py
tabermah 77.1 182 \\
ahenkel 42.1 183 )))
184 {{/layout-cell}}
185 {{/layout-section}}
186
187 {{layout-section ac:type="two_equal"}}
188 {{layout-cell}}
189 [[image:attach:20211212_233140.jpg||height="250"]]
190 {{/layout-cell}}
191
192 {{layout-cell}}
193 **Chopper → no Chopper**
194
tabermah 77.1 195 * decrease frequency by max. 10 Hz steps
ahenkel 42.1 196 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
197 * at frequency = 10 Hz, click "Stop"
tabermah 77.1 198 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
ahenkel 42.1 199
tabermah 77.1 200 (% style="color:#000000" %)**no Chopper → Chopper**
ahenkel 42.1 201
tabermah 77.1 202 * (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
203 * (% style="color:#000000" %)increase frequency by max. 10 Hz steps
204 ** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
205 * (% 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//
ahenkel 42.1 206 {{/layout-cell}}
207 {{/layout-section}}
208
ahenkel 59.1 209 {{layout-section ac:type="single"}}
ahenkel 42.1 210 {{layout-cell}}
ahenkel 69.1 211 ----
212
tabermah 79.6 213 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6 Data collection =
ahenkel 47.1 214
ahenkel 36.1 215 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
216
ahenkel 40.1 217 (% class="code" %)
218 (((
ahenkel 76.1 219 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
ahenkel 40.1 220 password: written on control laptop (changes every 6 months)
221 )))
ahenkel 36.1 222
ahenkel 51.1 223 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
ahenkel 36.1 224
tabermah 77.1 225
ahenkel 59.1 226 {{/layout-cell}}
227 {{/layout-section}}
ahenkel 12.1 228
ahenkel 59.1 229 {{layout-section ac:type="two_left_sidebar"}}
230 {{layout-cell}}
ahenkel 51.1 231 **Check list:**
ahenkel 40.1 232
tabermah 77.1 233 (% style="color:#ff0000" %)//always after entering the hutch!//
ahenkel 40.1 234
tabermah 77.1 235 (% style="color:#000000" %)Click "Run" icon in kamzik.
ahenkel 51.1 236
tabermah 77.1 237 * Put detector distance 200 in //prepare_for_measurement (      )//
238 * Click "<Call>" next to //prepare_for_measurement//
239 This will:
ahenkel 75.1 240 ** drive the collimator in //IN// position
241 ** drive detector to 200 mm
ahenkel 51.1 242
tabermah 77.1 243 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
ahenkel 51.1 244
ahenkel 68.1 245 //**Set run parameters and go 🏃💥**//
ahenkel 36.1 246
ahenkel 39.1 247 1. Set your desired No. of frames
ahenkel 76.1 248 1. Enter the protein ID of your crystal sample
ahenkel 67.1 249 1. Match exposure time with chopper setting or set desired exposure time
ahenkel 39.1 250 1. Check trigger setting and match to chopper setting
tabermah 77.1 251 no chopper → external triffer //off//
252 chopper → external trigger// on//
ahenkel 68.1 253 1. To start the run, click "<Call>" next to //start_run (exposure    )//
254 {{/layout-cell}}
ahenkel 40.1 255
ahenkel 68.1 256 {{layout-cell}}
ahenkel 69.1 257 [[image:attach:Kamzik_run(2).PNG]]
ahenkel 37.1 258 {{/layout-cell}}
ahenkel 68.1 259 {{/layout-section}}
ahenkel 37.1 260
ahenkel 71.1 261 {{layout-section ac:type="single"}}
ahenkel 37.1 262 {{layout-cell}}
tabermah 77.1 263 (% class="relative-table wrapped" style="width:55.9569%" %)
ahenkel 36.1 264 |=(((
265 Parameter
266 )))|=(((
267 explanation
268 )))|=(% colspan="1" %)(((
269 value
270 )))
271 |(((
272 Images number
273 )))|(((
ahenkel 74.1 274 number of frames you want to collect
ahenkel 36.1 275 )))|(% colspan="1" %)(((
276 usually 100k - 200k, but adjust according to hitrate
277
278 orientation: 10 % hitrate needs at least 100k images
279 )))
280 |(((
281 exposure
282 )))|(((
283 exposure time of Eiger
284
tabermah 77.1 285
ahenkel 36.1 286 )))|(% colspan="1" %)(((
ahenkel 76.1 287 with chopper         → opening time displayed in chopper GUI
ahenkel 36.1 288 no chopper            → 7.7 ms
289
290 ----
291 )))
292 |(((
293 run id
294 )))|(((
295 changes automatically
296 )))|(% colspan="1" %)(((
tabermah 77.1 297
ahenkel 36.1 298 )))
299 |(% colspan="1" %)(((
300 Detector distance
301 )))|(% colspan="1" %)(((
302 current detector postion readout
303 )))|(% colspan="1" %)(((
tabermah 77.1 304
ahenkel 36.1 305 )))
ahenkel 76.1 306 |(% colspan="1" %)(((
307 protein ID
308 )))|(% colspan="1" %)(((
309 protein ID of crystal sample (see AMARCORD)
310 )))|(% colspan="1" %)(((
tabermah 77.1 311
ahenkel 76.1 312 )))
ahenkel 68.1 313
ahenkel 71.1 314 ----
ahenkel 69.1 315 {{/layout-cell}}
316 {{/layout-section}}
317
318 {{layout-section ac:type="two_equal"}}
319 {{layout-cell}}
ahenkel 68.1 320 **After data collection/Before entering the exp. hutch:**
321
322 1. Go to "Safety" in kamzik.
323 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
324 11. Drive the collimator out
325 11. Drive the detector back to 1500 mm
326 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
327
ahenkel 70.1 328 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
ahenkel 68.1 329 {{/layout-cell}}
ahenkel 69.1 330
331 {{layout-cell}}
tabermah 77.1 332
ahenkel 72.1 333
334
335
336
337
ahenkel 69.1 338 [[image:attach:safety_kamzik.PNG]]
339 {{/layout-cell}}
ahenkel 37.1 340 {{/layout-section}}
ahenkel 36.1 341
ahenkel 37.1 342 {{layout-section ac:type="single"}}
343 {{layout-cell}}
ahenkel 41.1 344 ----
345
tabermah 79.6 346 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7 Troubleshooting =
ahenkel 29.1 347
348 * (((
tabermah 79.6 349 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
ahenkel 41.1 350
351 * Tape roll empty?
352 * motor connected (icon green)?
ahenkel 29.1 353 )))
ahenkel 41.1 354
ahenkel 29.1 355 * (((
tabermah 79.6 356 == {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
ahenkel 41.1 357
358 * displayed in green=connected?
359 * nozzle holder colliding somewhere?
360 * motor limits reached? → position displayed in red
ahenkel 29.1 361 )))
ahenkel 41.1 362
ahenkel 29.1 363 * (((
tabermah 80.1 364 == {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
ahenkel 41.1 365
366 * channel turned on?
367 * Sample empty?
368 * Nozzle or lines clogged? → flush with water, change nozzle
ahenkel 29.1 369 )))
ahenkel 51.1 370
ahenkel 49.1 371 * (((
tabermah 80.1 372 == {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
ahenkel 49.1 373
374 * First, restart kamzik (server+client) and see if this solves the issue
375 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
ahenkel 51.1 376 * (((
tabermah 77.1 377 If nothing works, kill the Simplon process and then start the server again:*
378
379 (((
ahenkel 51.1 380 (% class="code" %)
381 (((
382 ssh haspp11exp03
ahenkel 49.1 383 )))
ahenkel 51.1 384 )))
tabermah 77.1 385
ahenkel 51.1 386 * (((
387 (% class="code" %)
388 (((
389 ps -ef | grep Simplon
390 )))
391 )))
392 * (((
393 (% class="code" %)
394 (((
395 kill -9 simplon_process_id
396 )))
397 )))
398 )))
ahenkel 76.1 399 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
ahenkel 51.1 400 )))
ahenkel 37.1 401 {{/layout-cell}}
402 {{/layout-section}}
ahenkel 51.1 403
404 {{layout-section ac:type="single"}}
405 {{layout-cell}}
tabermah 77.1 406
ahenkel 51.1 407 {{/layout-cell}}
408 {{/layout-section}}
ahenkel 37.1 409 {{/layout}}