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Title
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1 -14. Serial Crystallography: CFEL TapeDrive
1 +08. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.ahenkel
1 +XWiki.chatzies
Content
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1 -**14.1 Revert from Crystallography to TapeDrive (P11 staff)**
1 +{{layout}}
2 +{{layout-section ac:type="single"}}
3 +{{layout-cell}}
4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
2 2  
3 -\\
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 +[[image:attach:kamzik_tape.PNG||height="400"]]
61 +
62 +
63 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
64 +
65 +* Click on the 'nozzle' icon.
66 +* (((
67 +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.
68 +The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
69 +
70 +
71 +(% 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" %)** !!!**(%%)
72 +\\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.
73 +
74 +(% class="wrapped" %)
75 +|=(((
76 +
77 +)))|=(((
78 +direction
79 +)))|=(((
80 +recommended step size
81 +for visual adjustment
82 +)))|=(% colspan="1" %)(((
83 +recommended step size
84 +during data collection
85 +)))
86 +|(((
87 ++x
88 +)))|(((
89 +away from X-ray interaction point
90 +)))|(((
91 +1.0 - 0.5 mm
92 +)))|(% colspan="1" %)(((
93 +0.1 - 0.2 mm
94 +)))
95 +|(((
96 ++y
97 +)))|(((
98 +up
99 +)))|(((
100 +1.0 - 0.5 mm
101 +)))|(% colspan="1" %)(((
102 +0.1 - 0.2 mm
103 +)))
104 +|(((
105 ++z
106 +)))|(((
107 +towards detector tower, away from tape
108 +)))|(((
109 +0.5 - 0.2 mm
110 +)))|(% colspan="1" %)(((
111 +0.1 - 0.2 mm
112 +be careful with -z, tape could be pushed out of focus
113 +)))
114 +
115 +
116 +)))
117 +
118 +[[image:attach:kamzik_nozzle.PNG||height="400"]]
119 +
120 +
121 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
122 +
123 +* The chiller circulates fluid through the gas nozzle.
124 +
125 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
126 +
127 +
128 +== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
129 +
130 +
131 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
132 +
133 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
134 + password: //written on control laptop (changes every 6 months)//
135 +
136 +
137 +
138 +----
139 +
140 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
141 +
142 +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).
143 +
144 +* Remove the (almost) empty feeder roll by pulling it upwards.
145 +* Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
146 +* Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
147 +* Cut the first cm of the new tape roll, directly behind the black sticky part.
148 +* 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.
149 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
150 +* Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
151 +* Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
152 +* Attach new tape to the empty roll by using some sticky tape.
153 +* Close tape stabilizer.
154 +* Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
155 +
156 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
157 +
158 +
159 +{{/layout-cell}}
160 +{{/layout-section}}
161 +
162 +{{layout-section ac:type="single"}}
163 +{{layout-cell}}
164 +----
165 +
166 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
167 +
168 +start chopper gui from terminal:
169 +
170 +(% class="code" %)
171 +(((
172 + cd /gpfs/local/shared/ChopperControl          
173 +)))
174 +
175 +(% class="code" %)
176 +(((
177 + python chopperControl.py
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 mm 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 +[[image:attach:safety_kamzik.PNG]]
330 +{{/layout-cell}}
331 +{{/layout-section}}
332 +
333 +{{layout-section ac:type="single"}}
334 +{{layout-cell}}
335 +----
336 +
337 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
338 +
339 +* (((
340 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
341 +
342 +* Tape roll empty?
343 +* motor connected (icon green)?
344 +)))
345 +
346 +* (((
347 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
348 +
349 +* displayed in green=connected?
350 +* nozzle holder colliding somewhere?
351 +* motor limits reached? → position displayed in red
352 +)))
353 +
354 +* (((
355 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
356 +
357 +* channel turned on?
358 +* Sample empty?
359 +* Nozzle or lines clogged? → flush with water, change nozzle
360 +)))
361 +
362 +* (((
363 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
364 +
365 +* First, restart kamzik (server+client) and see if this solves the issue
366 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
367 +* (((
368 +If nothing works, kill the Simplon process and then start the server again:*
369 +
370 +(((
371 +(% class="code" %)
372 +(((
373 +ssh haspp11exp03
374 +)))
375 +)))
376 +
377 +* (((
378 +(% class="code" %)
379 +(((
380 +ps -ef | grep Simplon
381 +)))
382 +)))
383 +* (((
384 +(% class="code" %)
385 +(((
386 +kill -9 simplon_process_id
387 +)))
388 +)))
389 +)))
390 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
391 +)))
392 +{{/layout-cell}}
393 +{{/layout-section}}
394 +{{/layout}}
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1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
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