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Last modified by chatzies on 2025-11-27 11:35
From version 2.1
edited by ahenkel
on 2021-11-30 10:29
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Title
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1 -14. 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 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}}
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1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
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