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Version 77.1 by tabermah on 2024-12-03 11:26
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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
ahenkel 46.1 7 {{toc minLevel="2"/}}
8
ahenkel 23.1 9
ahenkel 47.1 10 ----
11
ahenkel 45.1 12 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 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 77.1 25 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26
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 77.1 47 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48
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
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.
tabermah 77.1 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
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
120
ahenkel 17.1 121 )))
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
ahenkel 32.1 129 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
ahenkel 17.1 130
131
ahenkel 33.1 132 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
133
ahenkel 23.1 134
ahenkel 13.1 135 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
136
137 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
tabermah 77.1 138 password: //written on control laptop (changes every 6 months)//
ahenkel 13.1 139
ahenkel 6.1 140
141
ahenkel 47.1 142 ----
ahenkel 12.1 143
ahenkel 47.1 144 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
145
ahenkel 19.1 146 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 12.1 147
ahenkel 19.1 148 * Remove the (almost) empty feeder roll by pulling it upwards.
ahenkel 22.1 149 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
ahenkel 19.1 150 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
ahenkel 35.1 151 * Cut the first cm of the new tape roll, directly behind the black sticky part.
152 * 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 77.1 153 * Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
ahenkel 35.1 154 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
155 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
156 * Attach new tape to the empty roll by using some sticky tape.
ahenkel 22.1 157 * Close tape stabilizer.
ahenkel 35.1 158 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
ahenkel 19.1 159
tabermah 77.1 160 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
ahenkel 19.1 161
ahenkel 6.1 162
ahenkel 7.1 163
tabermah 77.1 164
ahenkel 43.1 165 {{/layout-cell}}
166 {{/layout-section}}
ahenkel 28.1 167
ahenkel 43.1 168 {{layout-section ac:type="single"}}
169 {{layout-cell}}
ahenkel 47.1 170 ----
ahenkel 12.1 171
ahenkel 47.1 172 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
173
ahenkel 42.1 174 start chopper gui from terminal:
ahenkel 28.1 175
ahenkel 42.1 176 (% class="code" %)
177 (((
tabermah 77.1 178 cd /gpfs/local/shared/ChopperControl          
ahenkel 42.1 179 )))
180
181 (% class="code" %)
182 (((
183 python chopperControl.py
tabermah 77.1 184 \\
ahenkel 42.1 185 )))
186 {{/layout-cell}}
187 {{/layout-section}}
188
189 {{layout-section ac:type="two_equal"}}
190 {{layout-cell}}
191 [[image:attach:20211212_233140.jpg||height="250"]]
192 {{/layout-cell}}
193
194 {{layout-cell}}
195 **Chopper → no Chopper**
196
tabermah 77.1 197 * decrease frequency by max. 10 Hz steps
ahenkel 42.1 198 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
199 * at frequency = 10 Hz, click "Stop"
tabermah 77.1 200 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
ahenkel 42.1 201
tabermah 77.1 202 (% style="color:#000000" %)**no Chopper → Chopper**
ahenkel 42.1 203
tabermah 77.1 204 * (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
205 * (% style="color:#000000" %)increase frequency by max. 10 Hz steps
206 ** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
207 * (% 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 42.1 208 {{/layout-cell}}
209 {{/layout-section}}
210
ahenkel 59.1 211 {{layout-section ac:type="single"}}
ahenkel 42.1 212 {{layout-cell}}
ahenkel 69.1 213 ----
214
ahenkel 47.1 215 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
216
ahenkel 36.1 217 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
218
ahenkel 40.1 219 (% class="code" %)
220 (((
ahenkel 76.1 221 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
ahenkel 40.1 222 password: written on control laptop (changes every 6 months)
223 )))
ahenkel 36.1 224
ahenkel 51.1 225 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
ahenkel 36.1 226
tabermah 77.1 227
ahenkel 59.1 228 {{/layout-cell}}
229 {{/layout-section}}
ahenkel 12.1 230
ahenkel 59.1 231 {{layout-section ac:type="two_left_sidebar"}}
232 {{layout-cell}}
ahenkel 51.1 233 **Check list:**
ahenkel 40.1 234
tabermah 77.1 235 (% style="color:#ff0000" %)//always after entering the hutch!//
ahenkel 40.1 236
tabermah 77.1 237 (% style="color:#000000" %)Click "Run" icon in kamzik.
ahenkel 51.1 238
tabermah 77.1 239 * Put detector distance 200 in //prepare_for_measurement (      )//
240 * Click "<Call>" next to //prepare_for_measurement//
241 This will:
ahenkel 75.1 242 ** drive the collimator in //IN// position
243 ** drive detector to 200 mm
ahenkel 51.1 244
245
tabermah 77.1 246 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
ahenkel 51.1 247
ahenkel 40.1 248
ahenkel 68.1 249 //**Set run parameters and go 🏃💥**//
ahenkel 36.1 250
ahenkel 39.1 251 1. Set your desired No. of frames
ahenkel 76.1 252 1. Enter the protein ID of your crystal sample
ahenkel 67.1 253 1. Match exposure time with chopper setting or set desired exposure time
ahenkel 39.1 254 1. Check trigger setting and match to chopper setting
tabermah 77.1 255 no chopper → external triffer //off//
256 chopper → external trigger// on//
ahenkel 68.1 257 1. To start the run, click "<Call>" next to //start_run (exposure    )//
258 {{/layout-cell}}
ahenkel 40.1 259
ahenkel 68.1 260 {{layout-cell}}
ahenkel 69.1 261 [[image:attach:Kamzik_run(2).PNG]]
ahenkel 37.1 262 {{/layout-cell}}
ahenkel 68.1 263 {{/layout-section}}
ahenkel 37.1 264
ahenkel 71.1 265 {{layout-section ac:type="single"}}
ahenkel 37.1 266 {{layout-cell}}
tabermah 77.1 267 (% class="relative-table wrapped" style="width:55.9569%" %)
ahenkel 36.1 268 |=(((
269 Parameter
270 )))|=(((
271 explanation
272 )))|=(% colspan="1" %)(((
273 value
274 )))
275 |(((
276 Images number
277 )))|(((
ahenkel 74.1 278 number of frames you want to collect
ahenkel 36.1 279 )))|(% colspan="1" %)(((
280 usually 100k - 200k, but adjust according to hitrate
281
282 orientation: 10 % hitrate needs at least 100k images
283 )))
284 |(((
285 exposure
286 )))|(((
287 exposure time of Eiger
288
tabermah 77.1 289
ahenkel 36.1 290 )))|(% colspan="1" %)(((
ahenkel 76.1 291 with chopper         → opening time displayed in chopper GUI
ahenkel 36.1 292 no chopper            → 7.7 ms
293
294 ----
295 )))
296 |(((
297 run id
298 )))|(((
299 changes automatically
300 )))|(% colspan="1" %)(((
tabermah 77.1 301
ahenkel 36.1 302 )))
303 |(% colspan="1" %)(((
304 Detector distance
305 )))|(% colspan="1" %)(((
306 current detector postion readout
307 )))|(% colspan="1" %)(((
tabermah 77.1 308
ahenkel 36.1 309 )))
ahenkel 76.1 310 |(% colspan="1" %)(((
311 protein ID
312 )))|(% colspan="1" %)(((
313 protein ID of crystal sample (see AMARCORD)
314 )))|(% colspan="1" %)(((
tabermah 77.1 315
ahenkel 76.1 316 )))
ahenkel 68.1 317
ahenkel 71.1 318 ----
ahenkel 69.1 319 {{/layout-cell}}
320 {{/layout-section}}
321
322 {{layout-section ac:type="two_equal"}}
323 {{layout-cell}}
ahenkel 68.1 324 **After data collection/Before entering the exp. hutch:**
325
326 1. Go to "Safety" in kamzik.
327 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
328 11. Drive the collimator out
329 11. Drive the detector back to 1500 mm
330 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
331
ahenkel 70.1 332 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
ahenkel 68.1 333 {{/layout-cell}}
ahenkel 69.1 334
335 {{layout-cell}}
tabermah 77.1 336
ahenkel 72.1 337
338
339
340
341
ahenkel 69.1 342 [[image:attach:safety_kamzik.PNG]]
343 {{/layout-cell}}
ahenkel 37.1 344 {{/layout-section}}
ahenkel 36.1 345
ahenkel 37.1 346 {{layout-section ac:type="single"}}
347 {{layout-cell}}
ahenkel 41.1 348 ----
349
ahenkel 47.1 350 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
ahenkel 29.1 351
352 * (((
353 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
ahenkel 41.1 354
355 * Tape roll empty?
356 * motor connected (icon green)?
ahenkel 29.1 357 )))
ahenkel 41.1 358
359
ahenkel 29.1 360 * (((
361 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
ahenkel 41.1 362
363 * displayed in green=connected?
364 * nozzle holder colliding somewhere?
365 * motor limits reached? → position displayed in red
ahenkel 29.1 366 )))
ahenkel 41.1 367
368
ahenkel 29.1 369 * (((
370 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
ahenkel 41.1 371
372 * channel turned on?
373 * Sample empty?
374 * Nozzle or lines clogged? → flush with water, change nozzle
ahenkel 29.1 375 )))
ahenkel 51.1 376
377
ahenkel 49.1 378 * (((
379 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
380
381 * First, restart kamzik (server+client) and see if this solves the issue
382 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
ahenkel 51.1 383 * (((
tabermah 77.1 384 If nothing works, kill the Simplon process and then start the server again:*
385
386 (((
ahenkel 51.1 387 (% class="code" %)
388 (((
389 ssh haspp11exp03
ahenkel 49.1 390 )))
ahenkel 51.1 391 )))
tabermah 77.1 392
ahenkel 51.1 393 * (((
394 (% class="code" %)
395 (((
396 ps -ef | grep Simplon
397 )))
398 )))
399 * (((
400 (% class="code" %)
401 (((
402 kill -9 simplon_process_id
403 )))
404 )))
405 )))
ahenkel 76.1 406 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
ahenkel 51.1 407 )))
ahenkel 37.1 408 {{/layout-cell}}
409 {{/layout-section}}
ahenkel 51.1 410
411 {{layout-section ac:type="single"}}
412 {{layout-cell}}
tabermah 77.1 413
ahenkel 51.1 414 {{/layout-cell}}
415 {{/layout-section}}
ahenkel 37.1 416 {{/layout}}