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Last modified by chatzies on 2025-11-27 11:35
From version 83.4
edited by tabermah
on 2024-12-10 15:50
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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 (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 +https://confluence.desy.de/spaces/11/pages/235031925/14. Serial Crystallography: CFEL TapeDrive
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