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Version 51.1 by ahenkel on 2022-04-04 19:45
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1 {{layout}}
2 {{layout-section ac:type="single"}}
3 {{layout-cell}}
4 [[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
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) 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 on 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 an 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**. //!!!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//
218 {{/layout-cell}}
219 {{/layout-section}}
220
221 {{layout-section ac:type="two_equal"}}
222 {{layout-cell}}
223 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
224
225 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
226
227 (% class="code" %)
228 (((
229 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
230 password: written on control laptop (changes every 6 months)
231 )))
232
233 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
234
235 \\
236
237 **Check list:**
238
239 (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
240
241 (% style="color: rgb(0,0,0);" %)Click "Safety" icon in kamzik.
242
243 * Put collimator in
244 ** Click "<Call>" next to //collimator_in//
245
246 \\
247
248 * Open beam shutter BS1 in //CrystalControl//
249 {{/layout-cell}}
250
251 {{layout-cell}}
252 [[image:attach:kamzik_safety.PNG||height="400"]]
253 {{/layout-cell}}
254 {{/layout-section}}
255
256 {{layout-section ac:type="single"}}
257 {{layout-cell}}
258 ----
259
260 Click "Start/Run" icon in kamzik.
261
262 [[image:attach:kamzik_run-tile.jpg||height="400"]]
263
264 ----
265 {{/layout-cell}}
266 {{/layout-section}}
267
268 {{layout-section ac:type="two_equal"}}
269 {{layout-cell}}
270 **Set run parameters and go 🏃💥**
271
272 1. Set your desired No. of frames
273 1. Match exposure time with chopper setting
274 1. Check trigger setting and match to chopper setting
275 1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
276 1. To start the run, click "<Call>" next to //exposure time//
277
278 \\
279
280 \\
281
282 **After data collection/before entering the exp. hutch**
283
284 1. Go to "Safety" in kamzik.
285 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
286 11. Drive the collimator out
287 11. Drive the detector back to 1500 mm
288 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
289
290 [[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
291 {{/layout-cell}}
292
293 {{layout-cell}}
294 (% class="wrapped relative-table" style="width: 100.0%;" %)
295 |=(((
296 Parameter
297 )))|=(((
298 explanation
299 )))|=(% colspan="1" %)(((
300 value
301 )))
302 |(((
303 Images number
304 )))|(((
305 Set number of frames you want to collect
306 )))|(% colspan="1" %)(((
307 usually 100k - 200k, but adjust according to hitrate
308
309 orientation: 10 % hitrate needs at least 100k images
310 )))
311 |(((
312 exposure
313 )))|(((
314 exposure time of Eiger
315
316 \\
317 )))|(% colspan="1" %)(((
318 chopper at 133 Hz → 3.7 ms
319
320 chopper at 66 Hz   → 7.7 ms
321
322 no chopper            → 7.7 ms
323
324 ----
325 )))
326 |(((
327 run id
328 )))|(((
329 changes automatically
330 )))|(% colspan="1" %)(((
331 \\
332 )))
333 |(% colspan="1" %)(((
334 Detector distance
335 )))|(% colspan="1" %)(((
336 current detector postion readout
337 )))|(% colspan="1" %)(((
338 \\
339 )))
340 |(% colspan="1" %)(((
341 move_detector (distance)
342 )))|(% colspan="1" %)(((
343 Set detector distance
344 )))|(% colspan="1" %)(((
345 200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
346 )))
347 |(% colspan="1" %)(((
348 Diode voltage
349 )))|(% colspan="1" %)(((
350 read out of diode
351 )))|(% colspan="1" %)(((
352 **~~ 0 !!! higher values indicate missaligned beam stop!!! 
353 Call local contact
354 **
355 )))
356 {{/layout-cell}}
357 {{/layout-section}}
358
359 {{layout-section ac:type="single"}}
360 {{layout-cell}}
361 ----
362
363 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
364
365 * (((
366 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
367
368 * Tape roll empty?
369 * motor connected (icon green)?
370 )))
371
372 \\
373
374 * (((
375 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
376
377 * displayed in green=connected?
378 * nozzle holder colliding somewhere?
379 * motor limits reached? → position displayed in red
380 )))
381
382 \\
383
384 * (((
385 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
386
387 * channel turned on?
388 * Sample empty?
389 * Nozzle or lines clogged? → flush with water, change nozzle
390 )))
391
392 \\
393
394 * (((
395 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
396
397 * First, restart kamzik (server+client) and see if this solves the issue
398 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
399 * (((
400 If nothing works, kill the Simplon process and then start the server again:* (((
401 (% class="code" %)
402 (((
403 ssh haspp11exp03
404 )))
405 )))
406 * (((
407 (% class="code" %)
408 (((
409 ps -ef | grep Simplon
410 )))
411 )))
412 * (((
413 (% class="code" %)
414 (((
415 kill -9 simplon_process_id
416 )))
417 )))
418 )))
419 )))
420 {{/layout-cell}}
421 {{/layout-section}}
422
423 {{layout-section ac:type="single"}}
424 {{layout-cell}}
425 \\
426 {{/layout-cell}}
427 {{/layout-section}}
428 {{/layout}}