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Last modified by chatzies on 2025-11-27 11:35
From version 82.1
edited by tabermah
on 2024-12-10 15:22
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To version 2.1
edited by ahenkel
on 2021-11-30 10:29
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Title
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1 -08. Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.tabermah
1 +XWiki.ahenkel
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/235031925/14. Serial Crystallography: CFEL TapeDrive
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