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Version 83.6 by tabermah on 2024-12-10 15:54
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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 {{/layout-cell}}
161 {{/layout-section}}
162
163 {{layout-section ac:type="single"}}
164 {{layout-cell}}
165 ----
166
167 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
168
169 start chopper gui from terminal:
170
171 (% class="code" %)
172 (((
173 cd /gpfs/local/shared/ChopperControl          
174 )))
175
176 (% class="code" %)
177 (((
178 python chopperControl.py
179 \\
180 )))
181 {{/layout-cell}}
182 {{/layout-section}}
183
184 {{layout-section ac:type="two_equal"}}
185 {{layout-cell}}
186 [[image:attach:20211212_233140.jpg||height="250"]]
187 {{/layout-cell}}
188
189 {{layout-cell}}
190 **Chopper → no Chopper**
191
192 * decrease frequency by max. 10 Hz steps
193 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
194 * at frequency = 10 Hz, click "Stop"
195 * set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
196
197 (% style="color:#000000" %)**no Chopper → Chopper**
198
199 * (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
200 * (% style="color:#000000" %)increase frequency by max. 10 Hz steps
201 ** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
202 * (% 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//
203 {{/layout-cell}}
204 {{/layout-section}}
205
206 {{layout-section ac:type="single"}}
207 {{layout-cell}}
208 ----
209
210 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
211
212 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
213
214 (% class="code" %)
215 (((
216 xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
217 password: written on control laptop (changes every 6 months)
218 )))
219
220 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
221
222
223 {{/layout-cell}}
224 {{/layout-section}}
225
226 {{layout-section ac:type="two_left_sidebar"}}
227 {{layout-cell}}
228 **Check list:**
229
230 (% style="color:#ff0000" %)//always after entering the hutch!//
231
232 (% style="color:#000000" %)Click "Run" icon in kamzik.
233
234 * Put detector distance 200 mm in //prepare_for_measurement (      )//
235 * Click "<Call>" next to //prepare_for_measurement//
236 This will:
237 ** drive the collimator in //IN// position
238 ** drive detector to 200 mm
239
240 * Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
241
242 //**Set run parameters and go 🏃💥**//
243
244 1. Set your desired No. of frames
245 1. Enter the protein ID of your crystal sample
246 1. Match exposure time with chopper setting or set desired exposure time
247 1. Check trigger setting and match to chopper setting
248 no chopper → external triffer //off//
249 chopper → external trigger// on//
250 1. To start the run, click "<Call>" next to //start_run (exposure    )//
251 {{/layout-cell}}
252
253 {{layout-cell}}
254 [[image:attach:Kamzik_run(2).PNG]]
255 {{/layout-cell}}
256 {{/layout-section}}
257
258 {{layout-section ac:type="single"}}
259 {{layout-cell}}
260 (% class="relative-table wrapped" style="width:55.9569%" %)
261 |=(((
262 Parameter
263 )))|=(((
264 explanation
265 )))|=(% colspan="1" %)(((
266 value
267 )))
268 |(((
269 Images number
270 )))|(((
271 number of frames you want to collect
272 )))|(% colspan="1" %)(((
273 usually 100k - 200k, but adjust according to hitrate
274
275 orientation: 10 % hitrate needs at least 100k images
276 )))
277 |(((
278 exposure
279 )))|(((
280 exposure time of Eiger
281
282
283 )))|(% colspan="1" %)(((
284 with chopper         → opening time displayed in chopper GUI
285 no chopper            → 7.7 ms
286
287 ----
288 )))
289 |(((
290 run id
291 )))|(((
292 changes automatically
293 )))|(% colspan="1" %)(((
294
295 )))
296 |(% colspan="1" %)(((
297 Detector distance
298 )))|(% colspan="1" %)(((
299 current detector postion readout
300 )))|(% colspan="1" %)(((
301
302 )))
303 |(% colspan="1" %)(((
304 protein ID
305 )))|(% colspan="1" %)(((
306 protein ID of crystal sample (see AMARCORD)
307 )))|(% colspan="1" %)(((
308
309 )))
310
311 ----
312 {{/layout-cell}}
313 {{/layout-section}}
314
315 {{layout-section ac:type="two_equal"}}
316 {{layout-cell}}
317 **After data collection/Before entering the exp. hutch:**
318
319 1. Go to "Safety" in kamzik.
320 1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
321 11. Drive the collimator out
322 11. Drive the detector back to 1500 mm
323 1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
324
325 [[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
326 {{/layout-cell}}
327
328 {{layout-cell}}
329
330
331 [[image:attach:safety_kamzik.PNG]]
332 {{/layout-cell}}
333 {{/layout-section}}
334
335 {{layout-section ac:type="single"}}
336 {{layout-cell}}
337 ----
338
339 = {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
340
341 * (((
342 == {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
343
344 * Tape roll empty?
345 * motor connected (icon green)?
346 )))
347
348 * (((
349 == {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
350
351 * displayed in green=connected?
352 * nozzle holder colliding somewhere?
353 * motor limits reached? → position displayed in red
354 )))
355
356 * (((
357 == {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
358
359 * channel turned on?
360 * Sample empty?
361 * Nozzle or lines clogged? → flush with water, change nozzle
362 )))
363
364 * (((
365 == {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
366
367 * First, restart kamzik (server+client) and see if this solves the issue
368 * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
369 * (((
370 If nothing works, kill the Simplon process and then start the server again:*
371
372 (((
373 (% class="code" %)
374 (((
375 ssh haspp11exp03
376 )))
377 )))
378
379 * (((
380 (% class="code" %)
381 (((
382 ps -ef | grep Simplon
383 )))
384 )))
385 * (((
386 (% class="code" %)
387 (((
388 kill -9 simplon_process_id
389 )))
390 )))
391 )))
392 * After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
393 )))
394 {{/layout-cell}}
395 {{/layout-section}}
396 {{/layout}}