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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.chatzies
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/}}
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 -{{/layout-cell}}
161 -{{/layout-section}}
162 -
163 -{{layout-section ac:type="single"}}
164 -{{layout-cell}}
165 -----
166 -
167 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
168 -
169 -start chopper gui from terminal:
170 -
171 -(% class="code" %)
172 -(((
173 - cd /gpfs/local/shared/ChopperControl          
174 -)))
175 -
176 -(% class="code" %)
177 -(((
178 - python chopperControl.py
179 -\\
180 -)))
181 -{{/layout-cell}}
182 -{{/layout-section}}
183 -
184 -{{layout-section ac:type="two_equal"}}
185 -{{layout-cell}}
186 - [[image:attach:20211212_233140.jpg||height="250"]]
187 -{{/layout-cell}}
188 -
189 -{{layout-cell}}
190 -**Chopper → no Chopper**
191 -
192 -* decrease frequency by max. 10 Hz steps
193 -** click arrow down 10x, "Set", arrow down 10x, "Set", ....
194 -* at frequency = 10 Hz, click "Stop"
195 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
196 -
197 -(% style="color:#000000" %)**no Chopper → Chopper**
198 -
199 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
200 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
201 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
202 -* (% 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//
203 -{{/layout-cell}}
204 -{{/layout-section}}
205 -
206 -{{layout-section ac:type="single"}}
207 -{{layout-cell}}
208 -----
209 -
210 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
211 -
212 -Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
213 -
214 -(% class="code" %)
215 -(((
216 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
217 - password: written on control laptop (changes every 6 months)
218 -)))
219 -
220 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
221 -
222 -
223 -{{/layout-cell}}
224 -{{/layout-section}}
225 -
226 -{{layout-section ac:type="two_left_sidebar"}}
227 -{{layout-cell}}
228 -**Check list:**
229 -
230 -(% style="color:#ff0000" %)//always after entering the hutch!//
231 -
232 -(% style="color:#000000" %)Click "Run" icon in kamzik.
233 -
234 -* Put detector distance 200 mm in //prepare_for_measurement (      )//
235 -* Click "<Call>" next to //prepare_for_measurement//
236 -This will:
237 -** drive the collimator in //IN// position
238 -** drive detector to 200 mm
239 -
240 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
241 -
242 -//**Set run parameters and go 🏃💥**//
243 -
244 -1. Set your desired No. of frames
245 -1. Enter the protein ID of your crystal sample
246 -1. Match exposure time with chopper setting or set desired exposure time
247 -1. Check trigger setting and match to chopper setting
248 -no chopper → external triffer //off//
249 - chopper → external trigger// on//
250 -1. To start the run, click "<Call>" next to //start_run (exposure    )//
251 -{{/layout-cell}}
252 -
253 -{{layout-cell}}
254 -[[image:attach:Kamzik_run(2).PNG]]
255 -{{/layout-cell}}
256 -{{/layout-section}}
257 -
258 -{{layout-section ac:type="single"}}
259 -{{layout-cell}}
260 -(% class="relative-table wrapped" style="width:55.9569%" %)
261 -|=(((
262 -Parameter
263 -)))|=(((
264 -explanation
265 -)))|=(% colspan="1" %)(((
266 -value
267 -)))
268 -|(((
269 -Images number
270 -)))|(((
271 -number of frames you want to collect
272 -)))|(% colspan="1" %)(((
273 -usually 100k - 200k, but adjust according to hitrate
274 -
275 -orientation: 10 % hitrate needs at least 100k images
276 -)))
277 -|(((
278 -exposure
279 -)))|(((
280 -exposure time of Eiger
281 -
282 -
283 -)))|(% colspan="1" %)(((
284 -with chopper         → opening time displayed in chopper GUI
285 -no chopper            → 7.7 ms
286 -
287 -----
288 -)))
289 -|(((
290 -run id
291 -)))|(((
292 -changes automatically
293 -)))|(% colspan="1" %)(((
294 -
295 -)))
296 -|(% colspan="1" %)(((
297 -Detector distance
298 -)))|(% colspan="1" %)(((
299 -current detector postion readout
300 -)))|(% colspan="1" %)(((
301 -
302 -)))
303 -|(% colspan="1" %)(((
304 -protein ID
305 -)))|(% colspan="1" %)(((
306 -protein ID of crystal sample (see AMARCORD)
307 -)))|(% colspan="1" %)(((
308 -
309 -)))
310 -
311 -----
312 -{{/layout-cell}}
313 -{{/layout-section}}
314 -
315 -{{layout-section ac:type="two_equal"}}
316 -{{layout-cell}}
317 -**After data collection/Before entering the exp. hutch:**
318 -
319 -1. Go to "Safety" in kamzik.
320 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
321 -11. Drive the collimator out
322 -11. Drive the detector back to 1500 mm
323 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
324 -
325 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
326 -{{/layout-cell}}
327 -
328 -{{layout-cell}}
329 -
330 -
331 -[[image:attach:safety_kamzik.PNG]]
332 -{{/layout-cell}}
333 -{{/layout-section}}
334 -
335 -{{layout-section ac:type="single"}}
336 -{{layout-cell}}
337 -----
338 -
339 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
340 -
341 -* (((
342 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
343 -
344 -* Tape roll empty?
345 -* motor connected (icon green)?
346 -)))
347 -
348 -* (((
349 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
350 -
351 -* displayed in green=connected?
352 -* nozzle holder colliding somewhere?
353 -* motor limits reached? → position displayed in red
354 -)))
355 -
356 -* (((
357 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
358 -
359 -* channel turned on?
360 -* Sample empty?
361 -* Nozzle or lines clogged? → flush with water, change nozzle
362 -)))
363 -
364 -* (((
365 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
366 -
367 -* First, restart kamzik (server+client) and see if this solves the issue
368 -* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
369 -* (((
370 -If nothing works, kill the Simplon process and then start the server again:*
371 -
372 -(((
373 -(% class="code" %)
374 -(((
375 -ssh haspp11exp03
376 -)))
377 -)))
378 -
379 -* (((
380 -(% class="code" %)
381 -(((
382 -ps -ef | grep Simplon
383 -)))
384 -)))
385 -* (((
386 -(% class="code" %)
387 -(((
388 -kill -9 simplon_process_id
389 -)))
390 -)))
391 -)))
392 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
393 -)))
394 -{{/layout-cell}}
395 -{{/layout-section}}
396 -{{/layout}}
3 +\\
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1 +https://confluence.desy.de/spaces/11/pages/235032181/14. Serial Crystallography: CFEL TapeDrive
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