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Version 80.1 by tabermah on 2024-12-10 15:20
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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 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"/}}8.2 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"/}}8.3 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 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
122
123 == {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
124
125 * The chiller circulates fluid through the gas nozzle.
126
127 == {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
128
129
130 == {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
131
132
133 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
134
135 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
136 password: //written on control laptop (changes every 6 months)//
137
138
139
140 ----
141
142 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4 Tape roll exchange =
143
144 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).
145
146 * Remove the (almost) empty feeder roll by pulling it upwards.
147 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
148 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
149 * Cut the first cm of the new tape roll, directly behind the black sticky part.
150 * 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.
151 * Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
152 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
153 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
154 * Attach new tape to the empty roll by using some sticky tape.
155 * Close tape stabilizer.
156 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
157
158 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
159
160
161
162
163 {{/layout-cell}}
164 {{/layout-section}}
165
166 {{layout-section ac:type="single"}}
167 {{layout-cell}}
168 ----
169
170 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5 Chopper =
171
172 start chopper gui from terminal:
173
174 (% class="code" %)
175 (((
176 cd /gpfs/local/shared/ChopperControl          
177 )))
178
179 (% class="code" %)
180 (((
181 python chopperControl.py
182 \\
183 )))
184 {{/layout-cell}}
185 {{/layout-section}}
186
187 {{layout-section ac:type="two_equal"}}
188 {{layout-cell}}
189 [[image:attach:20211212_233140.jpg||height="250"]]
190 {{/layout-cell}}
191
192 {{layout-cell}}
193 **Chopper → no Chopper**
194
195 * decrease frequency by max. 10 Hz steps
196 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
197 * at frequency = 10 Hz, click "Stop"
198 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
199
200 (% style="color:#000000" %)**no Chopper → Chopper**
201
202 * (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
203 * (% style="color:#000000" %)increase frequency by max. 10 Hz steps
204 ** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
205 * (% 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//
206 {{/layout-cell}}
207 {{/layout-section}}
208
209 {{layout-section ac:type="single"}}
210 {{layout-cell}}
211 ----
212
213 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6 Data collection =
214
215 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
216
217 (% class="code" %)
218 (((
219 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
220 password: written on control laptop (changes every 6 months)
221 )))
222
223 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
224
225
226 {{/layout-cell}}
227 {{/layout-section}}
228
229 {{layout-section ac:type="two_left_sidebar"}}
230 {{layout-cell}}
231 **Check list:**
232
233 (% style="color:#ff0000" %)//always after entering the hutch!//
234
235 (% style="color:#000000" %)Click "Run" icon in kamzik.
236
237 * Put detector distance 200 in //prepare_for_measurement (      )//
238 * Click "<Call>" next to //prepare_for_measurement//
239 This will:
240 ** drive the collimator in //IN// position
241 ** drive detector to 200 mm
242
243 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
244
245 //**Set run parameters and go 🏃💥**//
246
247 1. Set your desired No. of frames
248 1. Enter the protein ID of your crystal sample
249 1. Match exposure time with chopper setting or set desired exposure time
250 1. Check trigger setting and match to chopper setting
251 no chopper → external triffer //off//
252 chopper → external trigger// on//
253 1. To start the run, click "<Call>" next to //start_run (exposure    )//
254 {{/layout-cell}}
255
256 {{layout-cell}}
257 [[image:attach:Kamzik_run(2).PNG]]
258 {{/layout-cell}}
259 {{/layout-section}}
260
261 {{layout-section ac:type="single"}}
262 {{layout-cell}}
263 (% class="relative-table wrapped" style="width:55.9569%" %)
264 |=(((
265 Parameter
266 )))|=(((
267 explanation
268 )))|=(% colspan="1" %)(((
269 value
270 )))
271 |(((
272 Images number
273 )))|(((
274 number of frames you want to collect
275 )))|(% colspan="1" %)(((
276 usually 100k - 200k, but adjust according to hitrate
277
278 orientation: 10 % hitrate needs at least 100k images
279 )))
280 |(((
281 exposure
282 )))|(((
283 exposure time of Eiger
284
285
286 )))|(% colspan="1" %)(((
287 with chopper         → opening time displayed in chopper GUI
288 no chopper            → 7.7 ms
289
290 ----
291 )))
292 |(((
293 run id
294 )))|(((
295 changes automatically
296 )))|(% colspan="1" %)(((
297
298 )))
299 |(% colspan="1" %)(((
300 Detector distance
301 )))|(% colspan="1" %)(((
302 current detector postion readout
303 )))|(% colspan="1" %)(((
304
305 )))
306 |(% colspan="1" %)(((
307 protein ID
308 )))|(% colspan="1" %)(((
309 protein ID of crystal sample (see AMARCORD)
310 )))|(% colspan="1" %)(((
311
312 )))
313
314 ----
315 {{/layout-cell}}
316 {{/layout-section}}
317
318 {{layout-section ac:type="two_equal"}}
319 {{layout-cell}}
320 **After data collection/Before entering the exp. hutch:**
321
322 1. Go to "Safety" in kamzik.
323 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
324 11. Drive the collimator out
325 11. Drive the detector back to 1500 mm
326 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
327
328 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
329 {{/layout-cell}}
330
331 {{layout-cell}}
332
333
334
335
336
337
338 [[image:attach:safety_kamzik.PNG]]
339 {{/layout-cell}}
340 {{/layout-section}}
341
342 {{layout-section ac:type="single"}}
343 {{layout-cell}}
344 ----
345
346 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7 Troubleshooting =
347
348 * (((
349 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
350
351 * Tape roll empty?
352 * motor connected (icon green)?
353 )))
354
355 * (((
356 == {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
357
358 * displayed in green=connected?
359 * nozzle holder colliding somewhere?
360 * motor limits reached? → position displayed in red
361 )))
362
363 * (((
364 == {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
365
366 * channel turned on?
367 * Sample empty?
368 * Nozzle or lines clogged? → flush with water, change nozzle
369 )))
370
371 * (((
372 == {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
373
374 * First, restart kamzik (server+client) and see if this solves the issue
375 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
376 * (((
377 If nothing works, kill the Simplon process and then start the server again:*
378
379 (((
380 (% class="code" %)
381 (((
382 ssh haspp11exp03
383 )))
384 )))
385
386 * (((
387 (% class="code" %)
388 (((
389 ps -ef | grep Simplon
390 )))
391 )))
392 * (((
393 (% class="code" %)
394 (((
395 kill -9 simplon_process_id
396 )))
397 )))
398 )))
399 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
400 )))
401 {{/layout-cell}}
402 {{/layout-section}}
403
404 {{layout-section ac:type="single"}}
405 {{layout-cell}}
406
407 {{/layout-cell}}
408 {{/layout-section}}
409 {{/layout}}