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Version 67.1 by ahenkel on 2022-05-07 18:33
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1 {{layout}}
2 {{layout-section ac:type="single"}}
3 {{layout-cell}}
4 [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5
6 \\
7
8 {{toc minLevel="2"/}}
9
10 \\
11
12 ----
13
14 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
15
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.
17
18 Preparation:
19
20 * filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
21
22 [[image:attach:20211201_095534.jpg||height="250"]]
23
24 \\
25
26 ----
27
28 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 ** ==
30
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!**
32
33 Be aware to which channel and nozzle line your sample is connected.
34
35 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
36
37 Green → Channel 2, substrate line (nozzle capillary is marked in black)
38
39 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
40
41 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
42
43 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
44
45 \\
46
47 ----
48
49 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 ** ==
51
52 The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
53 Now start the client. Same thing, a terminal will open, shortly after a small window.
54
55 Click 'Devices' in the **client session** to open the control window.
56 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
57
58 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
59
60 * Click the 'main tape' icon
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.
64 \\
65 * [[image:attach:kamzik_tape.PNG||height="400"]]
66
67 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
68
69 * Click on the 'nozzle' icon.
70 * (((
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.
72 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
73
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
78 (% class="wrapped" %)
79 |=(((
80 \\
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 )))|(((
93 away from X-ray interaction point
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 )))
118
119 **
120 \\**
121 )))
122 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
123
124 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
125
126 * The chiller circulates fluid through the gas nozzle.
127
128 \\
129
130 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
131
132 \\
133
134 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
135
136 \\
137
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
144 \\
145
146 \\
147
148 ----
149
150 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151
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).
153
154 * Remove the (almost) empty feeder roll by pulling it upwards.
155 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
156 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
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.
159 * Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
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.
163 * Close tape stabilizer.
164 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
165
166 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 **
168
169 \\
170
171 \\
172
173 **
174 **
175 {{/layout-cell}}
176 {{/layout-section}}
177
178 {{layout-section ac:type="single"}}
179 {{layout-cell}}
180 ----
181
182 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183
184 start chopper gui from terminal:
185
186 (% class="code" %)
187 (((
188 cd /gpfs/local/shared/ChopperControl
189 )))
190
191 (% class="code" %)
192 (((
193 python chopperControl.py
194 \\\\
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", .....
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 //
219 {{/layout-cell}}
220 {{/layout-section}}
221
222 {{layout-section ac:type="single"}}
223 {{layout-cell}}
224 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
225
226 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
227
228 (% class="code" %)
229 (((
230 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
231 password: written on control laptop (changes every 6 months)
232 )))
233
234 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
235
236 \\
237 {{/layout-cell}}
238 {{/layout-section}}
239
240 {{layout-section ac:type="two_left_sidebar"}}
241 {{layout-cell}}
242 **Check list:**
243
244 (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
245
246 (% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
247
248 * Put collimator in
249 ** Put detector distance 200 in //prepare_for_measurement (      )
250 //
251 ** Click "<Call>" next to //prepare_for_measurement//
252
253 \\
254
255 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
256 {{/layout-cell}}
257
258 {{layout-cell}}
259 [[image:attach:kamzik_safety.PNG||height="400"]]
260 {{/layout-cell}}
261 {{/layout-section}}
262
263 {{layout-section ac:type="single"}}
264 {{layout-cell}}
265 ----
266
267 [[image:attach:kamzik_run-tile.jpg||height="400"]]
268
269 ----
270 {{/layout-cell}}
271 {{/layout-section}}
272
273 {{layout-section ac:type="two_equal"}}
274 {{layout-cell}}
275 **Set run parameters and go 🏃💥**
276
277 1. Set your desired No. of frames
278 1. Match exposure time with chopper setting or set desired exposure time
279 1. Check trigger setting and match to chopper setting
280 1. To start the run, click "<Call>" next to //start_run (exposure    )
281 //
282
283 \\
284
285 \\
286
287 **After data collection/Before entering the exp. hutch:**
288
289 1. Go to "Safety" in kamzik.
290 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
291 11. Drive the collimator out
292 11. Drive the detector back to 1500 mm
293 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
294
295 [[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
296 {{/layout-cell}}
297
298 {{layout-cell}}
299 (% class="wrapped relative-table" style="width: 100.0%;" %)
300 |=(((
301 Parameter
302 )))|=(((
303 explanation
304 )))|=(% colspan="1" %)(((
305 value
306 )))
307 |(((
308 Images number
309 )))|(((
310 Set number of frames you want to collect
311 )))|(% colspan="1" %)(((
312 usually 100k - 200k, but adjust according to hitrate
313
314 orientation: 10 % hitrate needs at least 100k images
315 )))
316 |(((
317 exposure
318 )))|(((
319 exposure time of Eiger
320
321 \\
322 )))|(% colspan="1" %)(((
323 chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
324
325 chopper at 66 Hz   → 7.7 ms
326
327 no chopper            → 7.7 ms
328
329 ----
330 )))
331 |(((
332 run id
333 )))|(((
334 changes automatically
335 )))|(% colspan="1" %)(((
336 \\
337 )))
338 |(% colspan="1" %)(((
339 Detector distance
340 )))|(% colspan="1" %)(((
341 current detector postion readout
342 )))|(% colspan="1" %)(((
343 \\
344 )))
345 |(% colspan="1" %)(((
346 move_detector (distance)
347 )))|(% colspan="1" %)(((
348 Set detector distance
349 )))|(% colspan="1" %)(((
350 200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
351 )))
352 {{/layout-cell}}
353 {{/layout-section}}
354
355 {{layout-section ac:type="single"}}
356 {{layout-cell}}
357 ----
358
359 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
360
361 * (((
362 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
363
364 * Tape roll empty?
365 * motor connected (icon green)?
366 )))
367
368 \\
369
370 * (((
371 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
372
373 * displayed in green=connected?
374 * nozzle holder colliding somewhere?
375 * motor limits reached? → position displayed in red
376 )))
377
378 \\
379
380 * (((
381 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
382
383 * channel turned on?
384 * Sample empty?
385 * Nozzle or lines clogged? → flush with water, change nozzle
386 )))
387
388 \\
389
390 * (((
391 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
392
393 * First, restart kamzik (server+client) and see if this solves the issue
394 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
395 * (((
396 If nothing works, kill the Simplon process and then start the server again:* (((
397 (% class="code" %)
398 (((
399 ssh haspp11exp03
400 )))
401 )))
402 * (((
403 (% class="code" %)
404 (((
405 ps -ef | grep Simplon
406 )))
407 )))
408 * (((
409 (% class="code" %)
410 (((
411 kill -9 simplon_process_id
412 )))
413 )))
414 )))
415 )))
416 {{/layout-cell}}
417 {{/layout-section}}
418
419 {{layout-section ac:type="single"}}
420 {{layout-cell}}
421 \\
422 {{/layout-cell}}
423 {{/layout-section}}
424 {{/layout}}