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Version 83.4 by tabermah on 2024-12-10 15:50
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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 81.1 12 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. Sample characteristics and preparation =
ahenkel 23.1 13
tabermah 83.1 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
tabermah 83.2 18 * filter through 30 µm (green) or 50 µm (yellow) cell filter into an 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 81.1 25 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}8.2. Connecting sample to ElveFlow, sample exchange =
tabermah 77.1 26
tabermah 83.2 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!**
ahenkel 5.1 28
ahenkel 21.1 29 Be aware to which channel and nozzle line your sample is connected.
30
ahenkel 31.1 31 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
ahenkel 21.1 32
ahenkel 22.1 33 Green → Channel 2, substrate line (nozzle capillary is marked in black)
ahenkel 21.1 34
35 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
36
ahenkel 28.1 37 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
ahenkel 5.1 38
ahenkel 28.1 39 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40
ahenkel 6.1 41
ahenkel 47.1 42 ----
43
tabermah 81.1 44 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. TapeDrive operation =
tabermah 77.1 45
tabermah 82.1 46 ​​​​​​The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
ahenkel 6.1 47
ahenkel 14.1 48 Now start the client. Same thing, a terminal will open, shortly after a small window.
ahenkel 16.1 49
50 Click 'Devices' in the **client session** to open the control window.
ahenkel 15.1 51 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
ahenkel 13.1 52
tabermah 79.5 53 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}Tape ==
ahenkel 14.1 54
ahenkel 63.1 55 * Click the 'main tape' icon
ahenkel 23.1 56 * Change the velocity by typing anything from **0.3-3.0 mm/s**
57 * Common velocity is 1.0-1.5 mm/s
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.
tabermah 77.1 59
ahenkel 14.1 60
tabermah 83.3 61 [[image:attach:kamzik_tape.PNG||height="400"]]
62
63
tabermah 79.5 64 == {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
ahenkel 23.1 65
ahenkel 62.1 66 * Click on the 'nozzle' icon.
ahenkel 23.1 67 * (((
ahenkel 19.1 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.
ahenkel 17.1 69 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
70
ahenkel 36.1 71
tabermah 83.3 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" %)** !!!**(%%)
ahenkel 36.1 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
ahenkel 44.1 75 (% class="wrapped" %)
ahenkel 17.1 76 |=(((
tabermah 77.1 77
ahenkel 17.1 78 )))|=(((
79 direction
80 )))|=(((
tabermah 77.1 81 recommended step size
ahenkel 17.1 82 for visual adjustment
83 )))|=(% colspan="1" %)(((
84 recommended step size
85 during data collection
86 )))
87 |(((
88 +x
89 )))|(((
ahenkel 18.1 90 away from X-ray interaction point
ahenkel 17.1 91 )))|(((
92 1.0 - 0.5 mm
93 )))|(% colspan="1" %)(((
94 0.1 - 0.2 mm
95 )))
96 |(((
97 +y
98 )))|(((
99 up
100 )))|(((
101 1.0 - 0.5 mm
102 )))|(% colspan="1" %)(((
103 0.1 - 0.2 mm
104 )))
105 |(((
106 +z
107 )))|(((
108 towards detector tower, away from tape
109 )))|(((
110 0.5 - 0.2 mm
111 )))|(% colspan="1" %)(((
112 0.1 - 0.2 mm
113 be careful with -z, tape could be pushed out of focus
114 )))
ahenkel 14.1 115
tabermah 77.1 116
ahenkel 17.1 117 )))
118
tabermah 83.3 119 [[image:attach:kamzik_nozzle.PNG||height="400"]]
120
121
tabermah 79.5 122 == {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
ahenkel 23.1 123
ahenkel 34.1 124 * The chiller circulates fluid through the gas nozzle.
ahenkel 30.1 125
tabermah 79.5 126 == {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
ahenkel 17.1 127
128
tabermah 79.6 129 == {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
ahenkel 33.1 130
ahenkel 23.1 131
ahenkel 13.1 132 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
133
134 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
tabermah 77.1 135 password: //written on control laptop (changes every 6 months)//
ahenkel 13.1 136
ahenkel 6.1 137
138
ahenkel 47.1 139 ----
ahenkel 12.1 140
tabermah 81.1 141 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
ahenkel 47.1 142
ahenkel 19.1 143 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).
ahenkel 12.1 144
ahenkel 19.1 145 * Remove the (almost) empty feeder roll by pulling it upwards.
ahenkel 22.1 146 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
ahenkel 19.1 147 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
ahenkel 35.1 148 * Cut the first cm of the new tape roll, directly behind the black sticky part.
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.
tabermah 77.1 150 * Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
ahenkel 35.1 151 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
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 * Attach new tape to the empty roll by using some sticky tape.
ahenkel 22.1 154 * Close tape stabilizer.
ahenkel 35.1 155 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
ahenkel 19.1 156
tabermah 77.1 157 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
ahenkel 19.1 158
ahenkel 6.1 159
ahenkel 7.1 160
tabermah 77.1 161
ahenkel 43.1 162 {{/layout-cell}}
163 {{/layout-section}}
ahenkel 28.1 164
ahenkel 43.1 165 {{layout-section ac:type="single"}}
166 {{layout-cell}}
ahenkel 47.1 167 ----
ahenkel 12.1 168
tabermah 81.1 169 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
ahenkel 47.1 170
ahenkel 42.1 171 start chopper gui from terminal:
ahenkel 28.1 172
ahenkel 42.1 173 (% class="code" %)
174 (((
tabermah 77.1 175 cd /gpfs/local/shared/ChopperControl          
ahenkel 42.1 176 )))
177
178 (% class="code" %)
179 (((
180 python chopperControl.py
tabermah 77.1 181 \\
ahenkel 42.1 182 )))
183 {{/layout-cell}}
184 {{/layout-section}}
185
186 {{layout-section ac:type="two_equal"}}
187 {{layout-cell}}
188 [[image:attach:20211212_233140.jpg||height="250"]]
189 {{/layout-cell}}
190
191 {{layout-cell}}
192 **Chopper → no Chopper**
193
tabermah 77.1 194 * decrease frequency by max. 10 Hz steps
ahenkel 42.1 195 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
196 * at frequency = 10 Hz, click "Stop"
tabermah 77.1 197 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
ahenkel 42.1 198
tabermah 77.1 199 (% style="color:#000000" %)**no Chopper → Chopper**
ahenkel 42.1 200
tabermah 77.1 201 * (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
202 * (% style="color:#000000" %)increase frequency by max. 10 Hz steps
203 ** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
204 * (% 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 42.1 205 {{/layout-cell}}
206 {{/layout-section}}
207
ahenkel 59.1 208 {{layout-section ac:type="single"}}
ahenkel 42.1 209 {{layout-cell}}
ahenkel 69.1 210 ----
211
tabermah 81.1 212 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
ahenkel 47.1 213
ahenkel 36.1 214 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
215
ahenkel 40.1 216 (% class="code" %)
217 (((
ahenkel 76.1 218 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
ahenkel 40.1 219 password: written on control laptop (changes every 6 months)
220 )))
ahenkel 36.1 221
ahenkel 51.1 222 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
ahenkel 36.1 223
tabermah 77.1 224
ahenkel 59.1 225 {{/layout-cell}}
226 {{/layout-section}}
ahenkel 12.1 227
ahenkel 59.1 228 {{layout-section ac:type="two_left_sidebar"}}
229 {{layout-cell}}
ahenkel 51.1 230 **Check list:**
ahenkel 40.1 231
tabermah 77.1 232 (% style="color:#ff0000" %)//always after entering the hutch!//
ahenkel 40.1 233
tabermah 77.1 234 (% style="color:#000000" %)Click "Run" icon in kamzik.
ahenkel 51.1 235
tabermah 77.1 236 * Put detector distance 200 in //prepare_for_measurement (      )//
237 * Click "<Call>" next to //prepare_for_measurement//
238 This will:
ahenkel 75.1 239 ** drive the collimator in //IN// position
240 ** drive detector to 200 mm
ahenkel 51.1 241
tabermah 77.1 242 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
ahenkel 51.1 243
ahenkel 68.1 244 //**Set run parameters and go 🏃💥**//
ahenkel 36.1 245
ahenkel 39.1 246 1. Set your desired No. of frames
ahenkel 76.1 247 1. Enter the protein ID of your crystal sample
ahenkel 67.1 248 1. Match exposure time with chopper setting or set desired exposure time
ahenkel 39.1 249 1. Check trigger setting and match to chopper setting
tabermah 77.1 250 no chopper → external triffer //off//
251 chopper → external trigger// on//
ahenkel 68.1 252 1. To start the run, click "<Call>" next to //start_run (exposure    )//
253 {{/layout-cell}}
ahenkel 40.1 254
ahenkel 68.1 255 {{layout-cell}}
ahenkel 69.1 256 [[image:attach:Kamzik_run(2).PNG]]
ahenkel 37.1 257 {{/layout-cell}}
ahenkel 68.1 258 {{/layout-section}}
ahenkel 37.1 259
ahenkel 71.1 260 {{layout-section ac:type="single"}}
ahenkel 37.1 261 {{layout-cell}}
tabermah 77.1 262 (% class="relative-table wrapped" style="width:55.9569%" %)
ahenkel 36.1 263 |=(((
264 Parameter
265 )))|=(((
266 explanation
267 )))|=(% colspan="1" %)(((
268 value
269 )))
270 |(((
271 Images number
272 )))|(((
ahenkel 74.1 273 number of frames you want to collect
ahenkel 36.1 274 )))|(% colspan="1" %)(((
275 usually 100k - 200k, but adjust according to hitrate
276
277 orientation: 10 % hitrate needs at least 100k images
278 )))
279 |(((
280 exposure
281 )))|(((
282 exposure time of Eiger
283
tabermah 77.1 284
ahenkel 36.1 285 )))|(% colspan="1" %)(((
ahenkel 76.1 286 with chopper         → opening time displayed in chopper GUI
ahenkel 36.1 287 no chopper            → 7.7 ms
288
289 ----
290 )))
291 |(((
292 run id
293 )))|(((
294 changes automatically
295 )))|(% colspan="1" %)(((
tabermah 77.1 296
ahenkel 36.1 297 )))
298 |(% colspan="1" %)(((
299 Detector distance
300 )))|(% colspan="1" %)(((
301 current detector postion readout
302 )))|(% colspan="1" %)(((
tabermah 77.1 303
ahenkel 36.1 304 )))
ahenkel 76.1 305 |(% colspan="1" %)(((
306 protein ID
307 )))|(% colspan="1" %)(((
308 protein ID of crystal sample (see AMARCORD)
309 )))|(% colspan="1" %)(((
tabermah 77.1 310
ahenkel 76.1 311 )))
ahenkel 68.1 312
ahenkel 71.1 313 ----
ahenkel 69.1 314 {{/layout-cell}}
315 {{/layout-section}}
316
317 {{layout-section ac:type="two_equal"}}
318 {{layout-cell}}
ahenkel 68.1 319 **After data collection/Before entering the exp. hutch:**
320
321 1. Go to "Safety" in kamzik.
322 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
323 11. Drive the collimator out
324 11. Drive the detector back to 1500 mm
325 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
326
ahenkel 70.1 327 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
ahenkel 68.1 328 {{/layout-cell}}
ahenkel 69.1 329
330 {{layout-cell}}
tabermah 77.1 331
ahenkel 72.1 332
333
334
335
336
ahenkel 69.1 337 [[image:attach:safety_kamzik.PNG]]
338 {{/layout-cell}}
ahenkel 37.1 339 {{/layout-section}}
ahenkel 36.1 340
ahenkel 37.1 341 {{layout-section ac:type="single"}}
342 {{layout-cell}}
ahenkel 41.1 343 ----
344
tabermah 81.1 345 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
ahenkel 29.1 346
347 * (((
tabermah 79.6 348 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
ahenkel 41.1 349
350 * Tape roll empty?
351 * motor connected (icon green)?
ahenkel 29.1 352 )))
ahenkel 41.1 353
ahenkel 29.1 354 * (((
tabermah 79.6 355 == {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
ahenkel 41.1 356
357 * displayed in green=connected?
358 * nozzle holder colliding somewhere?
359 * motor limits reached? → position displayed in red
ahenkel 29.1 360 )))
ahenkel 41.1 361
ahenkel 29.1 362 * (((
tabermah 80.1 363 == {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
ahenkel 41.1 364
365 * channel turned on?
366 * Sample empty?
367 * Nozzle or lines clogged? → flush with water, change nozzle
ahenkel 29.1 368 )))
ahenkel 51.1 369
ahenkel 49.1 370 * (((
tabermah 80.1 371 == {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
ahenkel 49.1 372
373 * First, restart kamzik (server+client) and see if this solves the issue
374 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
ahenkel 51.1 375 * (((
tabermah 77.1 376 If nothing works, kill the Simplon process and then start the server again:*
377
378 (((
ahenkel 51.1 379 (% class="code" %)
380 (((
381 ssh haspp11exp03
ahenkel 49.1 382 )))
ahenkel 51.1 383 )))
tabermah 77.1 384
ahenkel 51.1 385 * (((
386 (% class="code" %)
387 (((
388 ps -ef | grep Simplon
389 )))
390 )))
391 * (((
392 (% class="code" %)
393 (((
394 kill -9 simplon_process_id
395 )))
396 )))
397 )))
ahenkel 76.1 398 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
ahenkel 51.1 399 )))
ahenkel 37.1 400 {{/layout-cell}}
401 {{/layout-section}}
ahenkel 51.1 402
403 {{layout-section ac:type="single"}}
404 {{layout-cell}}
tabermah 77.1 405
ahenkel 51.1 406 {{/layout-cell}}
407 {{/layout-section}}
ahenkel 37.1 408 {{/layout}}