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Last modified by chatzies on 2025-11-27 11:35
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on 2021-11-30 10:55
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Title
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1 -10. 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"]]
1 +**14.1 Revert from Crystallography to TapeDrive (P11 staff)**
5 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}}
3 +\\
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1 -https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235032181/14. Serial Crystallography: CFEL TapeDrive