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Version 82.1 by tabermah on 2024-12-10 15:22
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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 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!**
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 * [[image:attach:kamzik_tape.PNG||height="400"]]
61
62 == {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
63
64 * Click on the 'nozzle' icon.
65 * (((
66 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.
67 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
68
69
70 (% 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" %)** !!!**(%%)
71 \\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.
72
73 (% class="wrapped" %)
74 |=(((
75
76 )))|=(((
77 direction
78 )))|=(((
79 recommended step size
80 for visual adjustment
81 )))|=(% colspan="1" %)(((
82 recommended step size
83 during data collection
84 )))
85 |(((
86 +x
87 )))|(((
88 away from X-ray interaction point
89 )))|(((
90 1.0 - 0.5 mm
91 )))|(% colspan="1" %)(((
92 0.1 - 0.2 mm
93 )))
94 |(((
95 +y
96 )))|(((
97 up
98 )))|(((
99 1.0 - 0.5 mm
100 )))|(% colspan="1" %)(((
101 0.1 - 0.2 mm
102 )))
103 |(((
104 +z
105 )))|(((
106 towards detector tower, away from tape
107 )))|(((
108 0.5 - 0.2 mm
109 )))|(% colspan="1" %)(((
110 0.1 - 0.2 mm
111 be careful with -z, tape could be pushed out of focus
112 )))
113
114
115 )))
116 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
117
118 == {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
119
120 * The chiller circulates fluid through the gas nozzle.
121
122 == {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
123
124
125 == {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
126
127
128 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
129
130 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
131 password: //written on control laptop (changes every 6 months)//
132
133
134
135 ----
136
137 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
138
139 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).
140
141 * Remove the (almost) empty feeder roll by pulling it upwards.
142 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
143 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
144 * Cut the first cm of the new tape roll, directly behind the black sticky part.
145 * 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.
146 * Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
147 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
148 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
149 * Attach new tape to the empty roll by using some sticky tape.
150 * Close tape stabilizer.
151 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
152
153 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
154
155
156
157
158 {{/layout-cell}}
159 {{/layout-section}}
160
161 {{layout-section ac:type="single"}}
162 {{layout-cell}}
163 ----
164
165 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
166
167 start chopper gui from terminal:
168
169 (% class="code" %)
170 (((
171 cd /gpfs/local/shared/ChopperControl          
172 )))
173
174 (% class="code" %)
175 (((
176 python chopperControl.py
177 \\
178 )))
179 {{/layout-cell}}
180 {{/layout-section}}
181
182 {{layout-section ac:type="two_equal"}}
183 {{layout-cell}}
184 [[image:attach:20211212_233140.jpg||height="250"]]
185 {{/layout-cell}}
186
187 {{layout-cell}}
188 **Chopper → no Chopper**
189
190 * decrease frequency by max. 10 Hz steps
191 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
192 * at frequency = 10 Hz, click "Stop"
193 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
194
195 (% style="color:#000000" %)**no Chopper → Chopper**
196
197 * (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
198 * (% style="color:#000000" %)increase frequency by max. 10 Hz steps
199 ** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
200 * (% 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//
201 {{/layout-cell}}
202 {{/layout-section}}
203
204 {{layout-section ac:type="single"}}
205 {{layout-cell}}
206 ----
207
208 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
209
210 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
211
212 (% class="code" %)
213 (((
214 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
215 password: written on control laptop (changes every 6 months)
216 )))
217
218 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
219
220
221 {{/layout-cell}}
222 {{/layout-section}}
223
224 {{layout-section ac:type="two_left_sidebar"}}
225 {{layout-cell}}
226 **Check list:**
227
228 (% style="color:#ff0000" %)//always after entering the hutch!//
229
230 (% style="color:#000000" %)Click "Run" icon in kamzik.
231
232 * Put detector distance 200 in //prepare_for_measurement (      )//
233 * Click "<Call>" next to //prepare_for_measurement//
234 This will:
235 ** drive the collimator in //IN// position
236 ** drive detector to 200 mm
237
238 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
239
240 //**Set run parameters and go 🏃💥**//
241
242 1. Set your desired No. of frames
243 1. Enter the protein ID of your crystal sample
244 1. Match exposure time with chopper setting or set desired exposure time
245 1. Check trigger setting and match to chopper setting
246 no chopper → external triffer //off//
247 chopper → external trigger// on//
248 1. To start the run, click "<Call>" next to //start_run (exposure    )//
249 {{/layout-cell}}
250
251 {{layout-cell}}
252 [[image:attach:Kamzik_run(2).PNG]]
253 {{/layout-cell}}
254 {{/layout-section}}
255
256 {{layout-section ac:type="single"}}
257 {{layout-cell}}
258 (% class="relative-table wrapped" style="width:55.9569%" %)
259 |=(((
260 Parameter
261 )))|=(((
262 explanation
263 )))|=(% colspan="1" %)(((
264 value
265 )))
266 |(((
267 Images number
268 )))|(((
269 number of frames you want to collect
270 )))|(% colspan="1" %)(((
271 usually 100k - 200k, but adjust according to hitrate
272
273 orientation: 10 % hitrate needs at least 100k images
274 )))
275 |(((
276 exposure
277 )))|(((
278 exposure time of Eiger
279
280
281 )))|(% colspan="1" %)(((
282 with chopper         → opening time displayed in chopper GUI
283 no chopper            → 7.7 ms
284
285 ----
286 )))
287 |(((
288 run id
289 )))|(((
290 changes automatically
291 )))|(% colspan="1" %)(((
292
293 )))
294 |(% colspan="1" %)(((
295 Detector distance
296 )))|(% colspan="1" %)(((
297 current detector postion readout
298 )))|(% colspan="1" %)(((
299
300 )))
301 |(% colspan="1" %)(((
302 protein ID
303 )))|(% colspan="1" %)(((
304 protein ID of crystal sample (see AMARCORD)
305 )))|(% colspan="1" %)(((
306
307 )))
308
309 ----
310 {{/layout-cell}}
311 {{/layout-section}}
312
313 {{layout-section ac:type="two_equal"}}
314 {{layout-cell}}
315 **After data collection/Before entering the exp. hutch:**
316
317 1. Go to "Safety" in kamzik.
318 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
319 11. Drive the collimator out
320 11. Drive the detector back to 1500 mm
321 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
322
323 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
324 {{/layout-cell}}
325
326 {{layout-cell}}
327
328
329
330
331
332
333 [[image:attach:safety_kamzik.PNG]]
334 {{/layout-cell}}
335 {{/layout-section}}
336
337 {{layout-section ac:type="single"}}
338 {{layout-cell}}
339 ----
340
341 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
342
343 * (((
344 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
345
346 * Tape roll empty?
347 * motor connected (icon green)?
348 )))
349
350 * (((
351 == {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
352
353 * displayed in green=connected?
354 * nozzle holder colliding somewhere?
355 * motor limits reached? → position displayed in red
356 )))
357
358 * (((
359 == {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
360
361 * channel turned on?
362 * Sample empty?
363 * Nozzle or lines clogged? → flush with water, change nozzle
364 )))
365
366 * (((
367 == {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
368
369 * First, restart kamzik (server+client) and see if this solves the issue
370 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
371 * (((
372 If nothing works, kill the Simplon process and then start the server again:*
373
374 (((
375 (% class="code" %)
376 (((
377 ssh haspp11exp03
378 )))
379 )))
380
381 * (((
382 (% class="code" %)
383 (((
384 ps -ef | grep Simplon
385 )))
386 )))
387 * (((
388 (% class="code" %)
389 (((
390 kill -9 simplon_process_id
391 )))
392 )))
393 )))
394 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
395 )))
396 {{/layout-cell}}
397 {{/layout-section}}
398
399 {{layout-section ac:type="single"}}
400 {{layout-cell}}
401
402 {{/layout-cell}}
403 {{/layout-section}}
404 {{/layout}}