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Version 83.4 by tabermah on 2024-12-10 15:50
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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/}}
8
9
10 ----
11
12 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. 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 (green) or 50 µm (yellow) cell filter into an 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"/}}8.2. Connecting sample to ElveFlow, sample exchange =
26
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!**
28
29 Be aware to which channel and nozzle line your sample is connected.
30
31 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
32
33 Green → Channel 2, substrate line (nozzle capillary is marked in black)
34
35 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
36
37 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
38
39 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40
41
42 ----
43
44 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. TapeDrive operation =
45
46 ​​​​​​The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
47
48 Now start the client. Same thing, a terminal will open, shortly after a small window.
49
50 Click 'Devices' in the **client session** to open the control window.
51 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
52
53 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}Tape ==
54
55 * Click the 'main tape' icon
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.
59
60
61 [[image:attach:kamzik_tape.PNG||height="400"]]
62
63
64 == {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
65
66 * Click on the 'nozzle' icon.
67 * (((
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.
69 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
70
71
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" %)** !!!**(%%)
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
75 (% class="wrapped" %)
76 |=(((
77
78 )))|=(((
79 direction
80 )))|=(((
81 recommended step size
82 for visual adjustment
83 )))|=(% colspan="1" %)(((
84 recommended step size
85 during data collection
86 )))
87 |(((
88 +x
89 )))|(((
90 away from X-ray interaction point
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 )))
115
116
117 )))
118
119 [[image:attach:kamzik_nozzle.PNG||height="400"]]
120
121
122 == {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
123
124 * The chiller circulates fluid through the gas nozzle.
125
126 == {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
127
128
129 == {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
130
131
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
135 password: //written on control laptop (changes every 6 months)//
136
137
138
139 ----
140
141 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
142
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).
144
145 * Remove the (almost) empty feeder roll by pulling it upwards.
146 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
147 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
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.
150 * Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
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.
154 * Close tape stabilizer.
155 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
156
157 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
158
159
160
161
162 {{/layout-cell}}
163 {{/layout-section}}
164
165 {{layout-section ac:type="single"}}
166 {{layout-cell}}
167 ----
168
169 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
170
171 start chopper gui from terminal:
172
173 (% class="code" %)
174 (((
175 cd /gpfs/local/shared/ChopperControl          
176 )))
177
178 (% class="code" %)
179 (((
180 python chopperControl.py
181 \\
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
194 * decrease frequency by max. 10 Hz steps
195 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
196 * at frequency = 10 Hz, click "Stop"
197 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
198
199 (% style="color:#000000" %)**no Chopper → Chopper**
200
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//
205 {{/layout-cell}}
206 {{/layout-section}}
207
208 {{layout-section ac:type="single"}}
209 {{layout-cell}}
210 ----
211
212 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
213
214 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
215
216 (% class="code" %)
217 (((
218 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
219 password: written on control laptop (changes every 6 months)
220 )))
221
222 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
223
224
225 {{/layout-cell}}
226 {{/layout-section}}
227
228 {{layout-section ac:type="two_left_sidebar"}}
229 {{layout-cell}}
230 **Check list:**
231
232 (% style="color:#ff0000" %)//always after entering the hutch!//
233
234 (% style="color:#000000" %)Click "Run" icon in kamzik.
235
236 * Put detector distance 200 in //prepare_for_measurement (      )//
237 * Click "<Call>" next to //prepare_for_measurement//
238 This will:
239 ** drive the collimator in //IN// position
240 ** drive detector to 200 mm
241
242 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
243
244 //**Set run parameters and go 🏃💥**//
245
246 1. Set your desired No. of frames
247 1. Enter the protein ID of your crystal sample
248 1. Match exposure time with chopper setting or set desired exposure time
249 1. Check trigger setting and match to chopper setting
250 no chopper → external triffer //off//
251 chopper → external trigger// on//
252 1. To start the run, click "<Call>" next to //start_run (exposure    )//
253 {{/layout-cell}}
254
255 {{layout-cell}}
256 [[image:attach:Kamzik_run(2).PNG]]
257 {{/layout-cell}}
258 {{/layout-section}}
259
260 {{layout-section ac:type="single"}}
261 {{layout-cell}}
262 (% class="relative-table wrapped" style="width:55.9569%" %)
263 |=(((
264 Parameter
265 )))|=(((
266 explanation
267 )))|=(% colspan="1" %)(((
268 value
269 )))
270 |(((
271 Images number
272 )))|(((
273 number of frames you want to collect
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
284
285 )))|(% colspan="1" %)(((
286 with chopper         → opening time displayed in chopper GUI
287 no chopper            → 7.7 ms
288
289 ----
290 )))
291 |(((
292 run id
293 )))|(((
294 changes automatically
295 )))|(% colspan="1" %)(((
296
297 )))
298 |(% colspan="1" %)(((
299 Detector distance
300 )))|(% colspan="1" %)(((
301 current detector postion readout
302 )))|(% colspan="1" %)(((
303
304 )))
305 |(% colspan="1" %)(((
306 protein ID
307 )))|(% colspan="1" %)(((
308 protein ID of crystal sample (see AMARCORD)
309 )))|(% colspan="1" %)(((
310
311 )))
312
313 ----
314 {{/layout-cell}}
315 {{/layout-section}}
316
317 {{layout-section ac:type="two_equal"}}
318 {{layout-cell}}
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
327 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
328 {{/layout-cell}}
329
330 {{layout-cell}}
331
332
333
334
335
336
337 [[image:attach:safety_kamzik.PNG]]
338 {{/layout-cell}}
339 {{/layout-section}}
340
341 {{layout-section ac:type="single"}}
342 {{layout-cell}}
343 ----
344
345 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
346
347 * (((
348 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
349
350 * Tape roll empty?
351 * motor connected (icon green)?
352 )))
353
354 * (((
355 == {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
356
357 * displayed in green=connected?
358 * nozzle holder colliding somewhere?
359 * motor limits reached? → position displayed in red
360 )))
361
362 * (((
363 == {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
364
365 * channel turned on?
366 * Sample empty?
367 * Nozzle or lines clogged? → flush with water, change nozzle
368 )))
369
370 * (((
371 == {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
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)
375 * (((
376 If nothing works, kill the Simplon process and then start the server again:*
377
378 (((
379 (% class="code" %)
380 (((
381 ssh haspp11exp03
382 )))
383 )))
384
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 )))
398 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
399 )))
400 {{/layout-cell}}
401 {{/layout-section}}
402
403 {{layout-section ac:type="single"}}
404 {{layout-cell}}
405
406 {{/layout-cell}}
407 {{/layout-section}}
408 {{/layout}}