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Last modified by chatzies on 2025-11-27 11:35
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edited by ahenkel
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Title
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1 -14. Serial Crystallography: CFEL TapeDrive
1 +10. 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 minLevel="2"/}}
8 +
9 +
10 +----
11 +
12 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 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"/}}**14.2 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"/}}**14.3 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 +)))
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 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
130 +
131 +
132 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
133 +
134 +
135 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
136 +
137 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
138 + password: //written on control laptop (changes every 6 months)//
139 +
140 +
141 +
142 +----
143 +
144 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
145 +
146 +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).
147 +
148 +* Remove the (almost) empty feeder roll by pulling it upwards.
149 +* Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
150 +* Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
151 +* Cut the first cm of the new tape roll, directly behind the black sticky part.
152 +* 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.
153 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
154 +* Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
155 +* Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
156 +* Attach new tape to the empty roll by using some sticky tape.
157 +* Close tape stabilizer.
158 +* Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
159 +
160 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
161 +
162 +
163 +
164 +
165 +{{/layout-cell}}
166 +{{/layout-section}}
167 +
168 +{{layout-section ac:type="single"}}
169 +{{layout-cell}}
170 +----
171 +
172 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
173 +
174 +start chopper gui from terminal:
175 +
176 +(% class="code" %)
177 +(((
178 + cd /gpfs/local/shared/ChopperControl          
179 +)))
180 +
181 +(% class="code" %)
182 +(((
183 + python chopperControl.py
184 +\\
185 +)))
186 +{{/layout-cell}}
187 +{{/layout-section}}
188 +
189 +{{layout-section ac:type="two_equal"}}
190 +{{layout-cell}}
191 + [[image:attach:20211212_233140.jpg||height="250"]]
192 +{{/layout-cell}}
193 +
194 +{{layout-cell}}
195 +**Chopper → no Chopper**
196 +
197 +* decrease frequency by max. 10 Hz steps
198 +** click arrow down 10x, "Set", arrow down 10x, "Set", ....
199 +* at frequency = 10 Hz, click "Stop"
200 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
201 +
202 +(% style="color:#000000" %)**no Chopper → Chopper**
203 +
204 +* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
205 +* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
206 +** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
207 +* (% 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//
208 +{{/layout-cell}}
209 +{{/layout-section}}
210 +
211 +{{layout-section ac:type="single"}}
212 +{{layout-cell}}
213 +----
214 +
215 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
216 +
217 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
218 +
219 +(% class="code" %)
220 +(((
221 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
222 + password: written on control laptop (changes every 6 months)
223 +)))
224 +
225 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
226 +
227 +
228 +{{/layout-cell}}
229 +{{/layout-section}}
230 +
231 +{{layout-section ac:type="two_left_sidebar"}}
232 +{{layout-cell}}
233 +**Check list:**
234 +
235 +(% style="color:#ff0000" %)//always after entering the hutch!//
236 +
237 +(% style="color:#000000" %)Click "Run" icon in kamzik.
238 +
239 +* Put detector distance 200 in //prepare_for_measurement (      )//
240 +* Click "<Call>" next to //prepare_for_measurement//
241 +This will:
242 +** drive the collimator in //IN// position
243 +** drive detector to 200 mm
244 +
245 +
246 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
247 +
248 +
249 +//**Set run parameters and go 🏃💥**//
250 +
251 +1. Set your desired No. of frames
252 +1. Enter the protein ID of your crystal sample
253 +1. Match exposure time with chopper setting or set desired exposure time
254 +1. Check trigger setting and match to chopper setting
255 +no chopper → external triffer //off//
256 + chopper → external trigger// on//
257 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
258 +{{/layout-cell}}
259 +
260 +{{layout-cell}}
261 +[[image:attach:Kamzik_run(2).PNG]]
262 +{{/layout-cell}}
263 +{{/layout-section}}
264 +
265 +{{layout-section ac:type="single"}}
266 +{{layout-cell}}
267 +(% class="relative-table wrapped" style="width:55.9569%" %)
268 +|=(((
269 +Parameter
270 +)))|=(((
271 +explanation
272 +)))|=(% colspan="1" %)(((
273 +value
274 +)))
275 +|(((
276 +Images number
277 +)))|(((
278 +number of frames you want to collect
279 +)))|(% colspan="1" %)(((
280 +usually 100k - 200k, but adjust according to hitrate
281 +
282 +orientation: 10 % hitrate needs at least 100k images
283 +)))
284 +|(((
285 +exposure
286 +)))|(((
287 +exposure time of Eiger
288 +
289 +
290 +)))|(% colspan="1" %)(((
291 +with chopper         → opening time displayed in chopper GUI
292 +no chopper            → 7.7 ms
293 +
294 +----
295 +)))
296 +|(((
297 +run id
298 +)))|(((
299 +changes automatically
300 +)))|(% colspan="1" %)(((
301 +
302 +)))
303 +|(% colspan="1" %)(((
304 +Detector distance
305 +)))|(% colspan="1" %)(((
306 +current detector postion readout
307 +)))|(% colspan="1" %)(((
308 +
309 +)))
310 +|(% colspan="1" %)(((
311 +protein ID
312 +)))|(% colspan="1" %)(((
313 +protein ID of crystal sample (see AMARCORD)
314 +)))|(% colspan="1" %)(((
315 +
316 +)))
317 +
318 +----
319 +{{/layout-cell}}
320 +{{/layout-section}}
321 +
322 +{{layout-section ac:type="two_equal"}}
323 +{{layout-cell}}
324 +**After data collection/Before entering the exp. hutch:**
325 +
326 +1. Go to "Safety" in kamzik.
327 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
328 +11. Drive the collimator out
329 +11. Drive the detector back to 1500 mm
330 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
331 +
332 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
333 +{{/layout-cell}}
334 +
335 +{{layout-cell}}
336 +
337 +
338 +
339 +
340 +
341 +
342 +[[image:attach:safety_kamzik.PNG]]
343 +{{/layout-cell}}
344 +{{/layout-section}}
345 +
346 +{{layout-section ac:type="single"}}
347 +{{layout-cell}}
348 +----
349 +
350 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
351 +
352 +* (((
353 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
354 +
355 +* Tape roll empty?
356 +* motor connected (icon green)?
357 +)))
358 +
359 +
360 +* (((
361 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
362 +
363 +* displayed in green=connected?
364 +* nozzle holder colliding somewhere?
365 +* motor limits reached? → position displayed in red
366 +)))
367 +
368 +
369 +* (((
370 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
371 +
372 +* channel turned on?
373 +* Sample empty?
374 +* Nozzle or lines clogged? → flush with water, change nozzle
375 +)))
376 +
377 +
378 +* (((
379 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
380 +
381 +* First, restart kamzik (server+client) and see if this solves the issue
382 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
383 +* (((
384 +If nothing works, kill the Simplon process and then start the server again:*
385 +
386 +(((
387 +(% class="code" %)
388 +(((
389 +ssh haspp11exp03
390 +)))
391 +)))
392 +
393 +* (((
394 +(% class="code" %)
395 +(((
396 +ps -ef | grep Simplon
397 +)))
398 +)))
399 +* (((
400 +(% class="code" %)
401 +(((
402 +kill -9 simplon_process_id
403 +)))
404 +)))
405 +)))
406 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
407 +)))
408 +{{/layout-cell}}
409 +{{/layout-section}}
410 +
411 +{{layout-section ac:type="single"}}
412 +{{layout-cell}}
413 +
414 +{{/layout-cell}}
415 +{{/layout-section}}
416 +{{/layout}}
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1 -https://confluence.desy.de/spaces/11/pages/235031925/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive