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Last modified by chatzies on 2025-11-27 11:35
From version 76.1
edited by ahenkel
on 2022-11-02 16:25
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To version 3.1
edited by ahenkel
on 2021-11-30 10:55
Change comment: There is no comment for this version

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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 6  \\
7 -
8 -{{toc minLevel="2"/}}
9 -
10 -\\
11 -
12 -----
13 -
14 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
15 -
16 -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.
17 -
18 -Preparation:
19 -
20 -* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
21 -
22 -[[image:attach:20211201_095534.jpg||height="250"]]
23 -
24 -\\
25 -
26 -----
27 -
28 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 -** ==
30 -
31 -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!**
32 -
33 -Be aware to which channel and nozzle line your sample is connected.
34 -
35 - Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
36 -
37 - Green → Channel 2, substrate line (nozzle capillary is marked in black)
38 -
39 -[[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
40 -
41 -After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
42 -
43 -[[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
44 -
45 -\\
46 -
47 -----
48 -
49 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
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: rgb(255,0,0);" %)**!!! **(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color: rgb(255,0,0);" %)** !!!**(%%)
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 -
130 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
131 -
132 -\\
133 -
134 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
135 -
136 -\\
137 -
138 -Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
139 -
140 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
141 - password: //written on control laptop (changes every 6 months)
142 -//
143 -
144 -\\
145 -
146 -\\
147 -
148 -----
149 -
150 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151 -
152 -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).
153 -
154 -* Remove the (almost) empty feeder roll by pulling it upwards.
155 -* Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
156 -* Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
157 -* Cut the first cm of the new tape roll, directly behind the black sticky part.
158 -* 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.
159 -* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
160 -* Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
161 -* Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
162 -* Attach new tape to the empty roll by using some sticky tape.
163 -* Close tape stabilizer.
164 -* Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
165 -
166 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 -**
168 -
169 -\\
170 -
171 -\\
172 -
173 -**
174 -**
175 -{{/layout-cell}}
176 -{{/layout-section}}
177 -
178 -{{layout-section ac:type="single"}}
179 -{{layout-cell}}
180 -----
181 -
182 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183 -
184 -start chopper gui from terminal:
185 -
186 -(% class="code" %)
187 -(((
188 - cd /gpfs/local/shared/ChopperControl
189 -)))
190 -
191 -(% class="code" %)
192 -(((
193 - python chopperControl.py
194 -\\\\
195 -)))
196 -{{/layout-cell}}
197 -{{/layout-section}}
198 -
199 -{{layout-section ac:type="two_equal"}}
200 -{{layout-cell}}
201 - [[image:attach:20211212_233140.jpg||height="250"]]
202 -{{/layout-cell}}
203 -
204 -{{layout-cell}}
205 -**Chopper → no Chopper**
206 -
207 -* decrease frequency by max. 10 Hz steps\\
208 -** click arrow down 10x, "Set", arrow down 10x, "Set", ....
209 -* at frequency = 10 Hz, click "Stop"
210 -* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
211 -
212 -(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
213 -
214 -* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
215 -* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
216 -** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
217 -* (% style="color: rgb(0,0,0);" %)//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
218 -//
219 -{{/layout-cell}}
220 -{{/layout-section}}
221 -
222 -{{layout-section ac:type="single"}}
223 -{{layout-cell}}
224 -----
225 -
226 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227 -
228 -Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
229 -
230 -(% class="code" %)
231 -(((
232 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
233 - password: written on control laptop (changes every 6 months)
234 -)))
235 -
236 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
237 -
238 -\\
239 -{{/layout-cell}}
240 -{{/layout-section}}
241 -
242 -{{layout-section ac:type="two_left_sidebar"}}
243 -{{layout-cell}}
244 -**Check list:**
245 -
246 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
247 -
248 -(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
249 -
250 -* Put detector distance 200 in //prepare_for_measurement (      )
251 -//
252 -* Click "<Call>" next to //prepare_for_measurement
253 -//This will:\\
254 -** drive the collimator in //IN// position
255 -** drive detector to 200 mm
256 -
257 -\\
258 -
259 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
260 -
261 -\\
262 -
263 -//**Set run parameters and go 🏃💥**//
264 -
265 -1. Set your desired No. of frames
266 -1. Enter the protein ID of your crystal sample
267 -1. Match exposure time with chopper setting or set desired exposure time
268 -1. Check trigger setting and match to chopper setting
269 -no chopper → external triffer //off
270 -// chopper → external trigger// on
271 -//
272 -1. To start the run, click "<Call>" next to //start_run (exposure    )//
273 -{{/layout-cell}}
274 -
275 -{{layout-cell}}
276 -[[image:attach:Kamzik_run(2).PNG]]
277 -{{/layout-cell}}
278 -{{/layout-section}}
279 -
280 -{{layout-section ac:type="single"}}
281 -{{layout-cell}}
282 -(% class="relative-table wrapped" style="width: 55.9569%;" %)
283 -|=(((
284 -Parameter
285 -)))|=(((
286 -explanation
287 -)))|=(% colspan="1" %)(((
288 -value
289 -)))
290 -|(((
291 -Images number
292 -)))|(((
293 -number of frames you want to collect
294 -)))|(% colspan="1" %)(((
295 -usually 100k - 200k, but adjust according to hitrate
296 -
297 -orientation: 10 % hitrate needs at least 100k images
298 -)))
299 -|(((
300 -exposure
301 -)))|(((
302 -exposure time of Eiger
303 -
304 -\\
305 -)))|(% colspan="1" %)(((
306 -with chopper         → opening time displayed in chopper GUI
307 -no chopper            → 7.7 ms
308 -
309 -----
310 -)))
311 -|(((
312 -run id
313 -)))|(((
314 -changes automatically
315 -)))|(% colspan="1" %)(((
316 -\\
317 -)))
318 -|(% colspan="1" %)(((
319 -Detector distance
320 -)))|(% colspan="1" %)(((
321 -current detector postion readout
322 -)))|(% colspan="1" %)(((
323 -\\
324 -)))
325 -|(% colspan="1" %)(((
326 -protein ID
327 -)))|(% colspan="1" %)(((
328 -protein ID of crystal sample (see AMARCORD)
329 -)))|(% colspan="1" %)(((
330 -\\
331 -)))
332 -
333 -----
334 -{{/layout-cell}}
335 -{{/layout-section}}
336 -
337 -{{layout-section ac:type="two_equal"}}
338 -{{layout-cell}}
339 -**After data collection/Before entering the exp. hutch:**
340 -
341 -1. Go to "Safety" in kamzik.
342 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
343 -11. Drive the collimator out
344 -11. Drive the detector back to 1500 mm
345 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
346 -
347 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
348 -{{/layout-cell}}
349 -
350 -{{layout-cell}}
351 -\\
352 -
353 -\\
354 -
355 -\\
356 -
357 -\\
358 -
359 -\\
360 -
361 -[[image:attach:safety_kamzik.PNG]]
362 -{{/layout-cell}}
363 -{{/layout-section}}
364 -
365 -{{layout-section ac:type="single"}}
366 -{{layout-cell}}
367 -----
368 -
369 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
370 -
371 -* (((
372 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
373 -
374 -* Tape roll empty?
375 -* motor connected (icon green)?
376 -)))
377 -
378 -\\
379 -
380 -* (((
381 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
382 -
383 -* displayed in green=connected?
384 -* nozzle holder colliding somewhere?
385 -* motor limits reached? → position displayed in red
386 -)))
387 -
388 -\\
389 -
390 -* (((
391 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
392 -
393 -* channel turned on?
394 -* Sample empty?
395 -* Nozzle or lines clogged? → flush with water, change nozzle
396 -)))
397 -
398 -\\
399 -
400 -* (((
401 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
402 -
403 -* First, restart kamzik (server+client) and see if this solves the issue
404 -* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
405 -* (((
406 -If nothing works, kill the Simplon process and then start the server again:* (((
407 -(% class="code" %)
408 -(((
409 -ssh haspp11exp03
410 -)))
411 -)))
412 -* (((
413 -(% class="code" %)
414 -(((
415 -ps -ef | grep Simplon
416 -)))
417 -)))
418 -* (((
419 -(% class="code" %)
420 -(((
421 -kill -9 simplon_process_id
422 -)))
423 -)))
424 -)))
425 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
426 -)))
427 -{{/layout-cell}}
428 -{{/layout-section}}
429 -
430 -{{layout-section ac:type="single"}}
431 -{{layout-cell}}
432 -\\
433 -{{/layout-cell}}
434 -{{/layout-section}}
435 -{{/layout}}
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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