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Last modified by chatzies on 2025-11-27 11:35
From version 1.1
edited by ahenkel
on 2021-11-30 10:29
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To version 76.1
edited by ahenkel
on 2022-11-02 16:25
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1 -Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Content
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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 +
8 +{{toc minLevel="2"/}}
9 +
10 +\\
11 +
12 +----
13 +
14 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
15 +
16 +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.
17 +
18 +Preparation:
19 +
20 +* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
21 +
22 +[[image:attach:20211201_095534.jpg||height="250"]]
23 +
24 +\\
25 +
26 +----
27 +
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
30 +
31 +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!**
32 +
33 +Be aware to which channel and nozzle line your sample is connected.
34 +
35 + Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
36 +
37 + Green → Channel 2, substrate line (nozzle capillary is marked in black)
38 +
39 +[[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
40 +
41 +After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
42 +
43 +[[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
44 +
45 +\\
46 +
47 +----
48 +
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
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: rgb(255,0,0);" %)**!!! **(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color: rgb(255,0,0);" %)** !!!**(%%)
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 +
130 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
131 +
132 +\\
133 +
134 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
135 +
136 +\\
137 +
138 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
139 +
140 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
141 + password: //written on control laptop (changes every 6 months)
142 +//
143 +
144 +\\
145 +
146 +\\
147 +
148 +----
149 +
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151 +
152 +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).
153 +
154 +* Remove the (almost) empty feeder roll by pulling it upwards.
155 +* Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
156 +* Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
157 +* Cut the first cm of the new tape roll, directly behind the black sticky part.
158 +* 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.
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
160 +* Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
161 +* Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
162 +* Attach new tape to the empty roll by using some sticky tape.
163 +* Close tape stabilizer.
164 +* Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
165 +
166 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 +**
168 +
169 +\\
170 +
171 +\\
172 +
173 +**
174 +**
175 +{{/layout-cell}}
176 +{{/layout-section}}
177 +
178 +{{layout-section ac:type="single"}}
179 +{{layout-cell}}
180 +----
181 +
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183 +
184 +start chopper gui from terminal:
185 +
186 +(% class="code" %)
187 +(((
188 + cd /gpfs/local/shared/ChopperControl
189 +)))
190 +
191 +(% class="code" %)
192 +(((
193 + python chopperControl.py
194 +\\\\
195 +)))
196 +{{/layout-cell}}
197 +{{/layout-section}}
198 +
199 +{{layout-section ac:type="two_equal"}}
200 +{{layout-cell}}
201 + [[image:attach:20211212_233140.jpg||height="250"]]
202 +{{/layout-cell}}
203 +
204 +{{layout-cell}}
205 +**Chopper → no Chopper**
206 +
207 +* decrease frequency by max. 10 Hz steps\\
208 +** click arrow down 10x, "Set", arrow down 10x, "Set", ....
209 +* at frequency = 10 Hz, click "Stop"
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
211 +
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
213 +
214 +* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
215 +* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
216 +** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
217 +* (% style="color: rgb(0,0,0);" %)//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
218 +//
219 +{{/layout-cell}}
220 +{{/layout-section}}
221 +
222 +{{layout-section ac:type="single"}}
223 +{{layout-cell}}
224 +----
225 +
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227 +
228 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
229 +
230 +(% class="code" %)
231 +(((
232 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
233 + password: written on control laptop (changes every 6 months)
234 +)))
235 +
236 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
237 +
238 +\\
239 +{{/layout-cell}}
240 +{{/layout-section}}
241 +
242 +{{layout-section ac:type="two_left_sidebar"}}
243 +{{layout-cell}}
244 +**Check list:**
245 +
246 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
247 +
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
249 +
250 +* Put detector distance 200 in //prepare_for_measurement (      )
251 +//
252 +* Click "<Call>" next to //prepare_for_measurement
253 +//This will:\\
254 +** drive the collimator in //IN// position
255 +** drive detector to 200 mm
256 +
257 +\\
258 +
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
260 +
261 +\\
262 +
263 +//**Set run parameters and go 🏃💥**//
264 +
265 +1. Set your desired No. of frames
266 +1. Enter the protein ID of your crystal sample
267 +1. Match exposure time with chopper setting or set desired exposure time
268 +1. Check trigger setting and match to chopper setting
269 +no chopper → external triffer //off
270 +// chopper → external trigger// on
271 +//
272 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
273 +{{/layout-cell}}
274 +
275 +{{layout-cell}}
276 +[[image:attach:Kamzik_run(2).PNG]]
277 +{{/layout-cell}}
278 +{{/layout-section}}
279 +
280 +{{layout-section ac:type="single"}}
281 +{{layout-cell}}
282 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
283 +|=(((
284 +Parameter
285 +)))|=(((
286 +explanation
287 +)))|=(% colspan="1" %)(((
288 +value
289 +)))
290 +|(((
291 +Images number
292 +)))|(((
293 +number of frames you want to collect
294 +)))|(% colspan="1" %)(((
295 +usually 100k - 200k, but adjust according to hitrate
296 +
297 +orientation: 10 % hitrate needs at least 100k images
298 +)))
299 +|(((
300 +exposure
301 +)))|(((
302 +exposure time of Eiger
303 +
304 +\\
305 +)))|(% colspan="1" %)(((
306 +with chopper         → opening time displayed in chopper GUI
307 +no chopper            → 7.7 ms
308 +
309 +----
310 +)))
311 +|(((
312 +run id
313 +)))|(((
314 +changes automatically
315 +)))|(% colspan="1" %)(((
316 +\\
317 +)))
318 +|(% colspan="1" %)(((
319 +Detector distance
320 +)))|(% colspan="1" %)(((
321 +current detector postion readout
322 +)))|(% colspan="1" %)(((
323 +\\
324 +)))
325 +|(% colspan="1" %)(((
326 +protein ID
327 +)))|(% colspan="1" %)(((
328 +protein ID of crystal sample (see AMARCORD)
329 +)))|(% colspan="1" %)(((
330 +\\
331 +)))
332 +
333 +----
334 +{{/layout-cell}}
335 +{{/layout-section}}
336 +
337 +{{layout-section ac:type="two_equal"}}
338 +{{layout-cell}}
339 +**After data collection/Before entering the exp. hutch:**
340 +
341 +1. Go to "Safety" in kamzik.
342 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
343 +11. Drive the collimator out
344 +11. Drive the detector back to 1500 mm
345 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
346 +
347 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
348 +{{/layout-cell}}
349 +
350 +{{layout-cell}}
351 +\\
352 +
353 +\\
354 +
355 +\\
356 +
357 +\\
358 +
359 +\\
360 +
361 +[[image:attach:safety_kamzik.PNG]]
362 +{{/layout-cell}}
363 +{{/layout-section}}
364 +
365 +{{layout-section ac:type="single"}}
366 +{{layout-cell}}
367 +----
368 +
369 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
370 +
371 +* (((
372 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
373 +
374 +* Tape roll empty?
375 +* motor connected (icon green)?
376 +)))
377 +
378 +\\
379 +
380 +* (((
381 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
382 +
383 +* displayed in green=connected?
384 +* nozzle holder colliding somewhere?
385 +* motor limits reached? → position displayed in red
386 +)))
387 +
388 +\\
389 +
390 +* (((
391 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
392 +
393 +* channel turned on?
394 +* Sample empty?
395 +* Nozzle or lines clogged? → flush with water, change nozzle
396 +)))
397 +
398 +\\
399 +
400 +* (((
401 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
402 +
403 +* First, restart kamzik (server+client) and see if this solves the issue
404 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
405 +* (((
406 +If nothing works, kill the Simplon process and then start the server again:* (((
407 +(% class="code" %)
408 +(((
409 +ssh haspp11exp03
410 +)))
411 +)))
412 +* (((
413 +(% class="code" %)
414 +(((
415 +ps -ef | grep Simplon
416 +)))
417 +)))
418 +* (((
419 +(% class="code" %)
420 +(((
421 +kill -9 simplon_process_id
422 +)))
423 +)))
424 +)))
425 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
426 +)))
427 +{{/layout-cell}}
428 +{{/layout-section}}
429 +
430 +{{layout-section ac:type="single"}}
431 +{{layout-cell}}
432 +\\
433 +{{/layout-cell}}
434 +{{/layout-section}}
435 +{{/layout}}
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Id
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1 -235031814
1 +235031805
Title
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1 -Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
URL
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1 -https://confluence.desy.de/spaces/11/pages/235031814/Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive