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Version 77.1 by tabermah on 2024-12-03 11:26
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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 {{toc minLevel="2"/}}
8
9
10 ----
11
12 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
13
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.
15
16 Preparation:
17
18 * filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
19
20 [[image:attach:20211201_095534.jpg||height="250"]]
21
22
23 ----
24
25 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26
27 *
28 ** ==
29
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!**
31
32 Be aware to which channel and nozzle line your sample is connected.
33
34 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
35
36 Green → Channel 2, substrate line (nozzle capillary is marked in black)
37
38 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
39
40 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
41
42 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
43
44
45 ----
46
47 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48
49 *
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:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
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 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
130
131
132 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
133
134
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
138 password: //written on control laptop (changes every 6 months)//
139
140
141
142 ----
143
144 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
145
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).
147
148 * Remove the (almost) empty feeder roll by pulling it upwards.
149 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
150 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
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.
153 * Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
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.
157 * Close tape stabilizer.
158 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
159
160 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
161
162
163
164
165 {{/layout-cell}}
166 {{/layout-section}}
167
168 {{layout-section ac:type="single"}}
169 {{layout-cell}}
170 ----
171
172 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
173
174 start chopper gui from terminal:
175
176 (% class="code" %)
177 (((
178 cd /gpfs/local/shared/ChopperControl          
179 )))
180
181 (% class="code" %)
182 (((
183 python chopperControl.py
184 \\
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
197 * decrease frequency by max. 10 Hz steps
198 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
199 * at frequency = 10 Hz, click "Stop"
200 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
201
202 (% style="color:#000000" %)**no Chopper → Chopper**
203
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//
208 {{/layout-cell}}
209 {{/layout-section}}
210
211 {{layout-section ac:type="single"}}
212 {{layout-cell}}
213 ----
214
215 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
216
217 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
218
219 (% class="code" %)
220 (((
221 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
222 password: written on control laptop (changes every 6 months)
223 )))
224
225 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
226
227
228 {{/layout-cell}}
229 {{/layout-section}}
230
231 {{layout-section ac:type="two_left_sidebar"}}
232 {{layout-cell}}
233 **Check list:**
234
235 (% style="color:#ff0000" %)//always after entering the hutch!//
236
237 (% style="color:#000000" %)Click "Run" icon in kamzik.
238
239 * Put detector distance 200 in //prepare_for_measurement (      )//
240 * Click "<Call>" next to //prepare_for_measurement//
241 This will:
242 ** drive the collimator in //IN// position
243 ** drive detector to 200 mm
244
245
246 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
247
248
249 //**Set run parameters and go 🏃💥**//
250
251 1. Set your desired No. of frames
252 1. Enter the protein ID of your crystal sample
253 1. Match exposure time with chopper setting or set desired exposure time
254 1. Check trigger setting and match to chopper setting
255 no chopper → external triffer //off//
256 chopper → external trigger// on//
257 1. To start the run, click "<Call>" next to //start_run (exposure    )//
258 {{/layout-cell}}
259
260 {{layout-cell}}
261 [[image:attach:Kamzik_run(2).PNG]]
262 {{/layout-cell}}
263 {{/layout-section}}
264
265 {{layout-section ac:type="single"}}
266 {{layout-cell}}
267 (% class="relative-table wrapped" style="width:55.9569%" %)
268 |=(((
269 Parameter
270 )))|=(((
271 explanation
272 )))|=(% colspan="1" %)(((
273 value
274 )))
275 |(((
276 Images number
277 )))|(((
278 number of frames you want to collect
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
289
290 )))|(% colspan="1" %)(((
291 with chopper         → opening time displayed in chopper GUI
292 no chopper            → 7.7 ms
293
294 ----
295 )))
296 |(((
297 run id
298 )))|(((
299 changes automatically
300 )))|(% colspan="1" %)(((
301
302 )))
303 |(% colspan="1" %)(((
304 Detector distance
305 )))|(% colspan="1" %)(((
306 current detector postion readout
307 )))|(% colspan="1" %)(((
308
309 )))
310 |(% colspan="1" %)(((
311 protein ID
312 )))|(% colspan="1" %)(((
313 protein ID of crystal sample (see AMARCORD)
314 )))|(% colspan="1" %)(((
315
316 )))
317
318 ----
319 {{/layout-cell}}
320 {{/layout-section}}
321
322 {{layout-section ac:type="two_equal"}}
323 {{layout-cell}}
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
332 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
333 {{/layout-cell}}
334
335 {{layout-cell}}
336
337
338
339
340
341
342 [[image:attach:safety_kamzik.PNG]]
343 {{/layout-cell}}
344 {{/layout-section}}
345
346 {{layout-section ac:type="single"}}
347 {{layout-cell}}
348 ----
349
350 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
351
352 * (((
353 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
354
355 * Tape roll empty?
356 * motor connected (icon green)?
357 )))
358
359
360 * (((
361 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
362
363 * displayed in green=connected?
364 * nozzle holder colliding somewhere?
365 * motor limits reached? → position displayed in red
366 )))
367
368
369 * (((
370 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
371
372 * channel turned on?
373 * Sample empty?
374 * Nozzle or lines clogged? → flush with water, change nozzle
375 )))
376
377
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)
383 * (((
384 If nothing works, kill the Simplon process and then start the server again:*
385
386 (((
387 (% class="code" %)
388 (((
389 ssh haspp11exp03
390 )))
391 )))
392
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 )))
406 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
407 )))
408 {{/layout-cell}}
409 {{/layout-section}}
410
411 {{layout-section ac:type="single"}}
412 {{layout-cell}}
413
414 {{/layout-cell}}
415 {{/layout-section}}
416 {{/layout}}