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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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on 2024-12-10 15:50
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Title
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1 -Serial Crystallography: CFEL TapeDrive
1 +08. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.ahenkel
1 +XWiki.tabermah
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 +{{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}}
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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
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