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1 -Serial Crystallography: CFEL TapeDrive
1 +08. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.ahenkel
1 +XWiki.tabermah
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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 minLevel="2"/}}
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 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"/}}**8.2 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"/}}**8.3 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 +* [[image:attach:kamzik_nozzle.PNG||height="400"]]
122 +
123 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
124 +
125 +* The chiller circulates fluid through the gas nozzle.
126 +
127 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
128 +
129 +
130 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
131 +
132 +
133 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
134 +
135 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
136 + password: //written on control laptop (changes every 6 months)//
137 +
138 +
139 +
140 +----
141 +
142 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**8.4 Tape roll exchange** ==
143 +
144 +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).
145 +
146 +* Remove the (almost) empty feeder roll by pulling it upwards.
147 +* Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
148 +* Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
149 +* Cut the first cm of the new tape roll, directly behind the black sticky part.
150 +* 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.
151 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
152 +* Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
153 +* Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
154 +* Attach new tape to the empty roll by using some sticky tape.
155 +* Close tape stabilizer.
156 +* Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
157 +
158 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
159 +
160 +
161 +
162 +
163 +{{/layout-cell}}
164 +{{/layout-section}}
165 +
166 +{{layout-section ac:type="single"}}
167 +{{layout-cell}}
168 +----
169 +
170 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**8.5 Chopper** ==
171 +
172 +start chopper gui from terminal:
173 +
174 +(% class="code" %)
175 +(((
176 + cd /gpfs/local/shared/ChopperControl          
177 +)))
178 +
179 +(% class="code" %)
180 +(((
181 + python chopperControl.py
182 +\\
183 +)))
184 +{{/layout-cell}}
185 +{{/layout-section}}
186 +
187 +{{layout-section ac:type="two_equal"}}
188 +{{layout-cell}}
189 + [[image:attach:20211212_233140.jpg||height="250"]]
190 +{{/layout-cell}}
191 +
192 +{{layout-cell}}
193 +**Chopper → no Chopper**
194 +
195 +* decrease frequency by max. 10 Hz steps
196 +** click arrow down 10x, "Set", arrow down 10x, "Set", ....
197 +* at frequency = 10 Hz, click "Stop"
198 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
199 +
200 +(% style="color:#000000" %)**no Chopper → Chopper**
201 +
202 +* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
203 +* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
204 +** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
205 +* (% 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//
206 +{{/layout-cell}}
207 +{{/layout-section}}
208 +
209 +{{layout-section ac:type="single"}}
210 +{{layout-cell}}
211 +----
212 +
213 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**8.6 Data collection** ==
214 +
215 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
216 +
217 +(% class="code" %)
218 +(((
219 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
220 + password: written on control laptop (changes every 6 months)
221 +)))
222 +
223 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
224 +
225 +
226 +{{/layout-cell}}
227 +{{/layout-section}}
228 +
229 +{{layout-section ac:type="two_left_sidebar"}}
230 +{{layout-cell}}
231 +**Check list:**
232 +
233 +(% style="color:#ff0000" %)//always after entering the hutch!//
234 +
235 +(% style="color:#000000" %)Click "Run" icon in kamzik.
236 +
237 +* Put detector distance 200 in //prepare_for_measurement (      )//
238 +* Click "<Call>" next to //prepare_for_measurement//
239 +This will:
240 +** drive the collimator in //IN// position
241 +** drive detector to 200 mm
242 +
243 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
244 +
245 +//**Set run parameters and go 🏃💥**//
246 +
247 +1. Set your desired No. of frames
248 +1. Enter the protein ID of your crystal sample
249 +1. Match exposure time with chopper setting or set desired exposure time
250 +1. Check trigger setting and match to chopper setting
251 +no chopper → external triffer //off//
252 + chopper → external trigger// on//
253 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
254 +{{/layout-cell}}
255 +
256 +{{layout-cell}}
257 +[[image:attach:Kamzik_run(2).PNG]]
258 +{{/layout-cell}}
259 +{{/layout-section}}
260 +
261 +{{layout-section ac:type="single"}}
262 +{{layout-cell}}
263 +(% class="relative-table wrapped" style="width:55.9569%" %)
264 +|=(((
265 +Parameter
266 +)))|=(((
267 +explanation
268 +)))|=(% colspan="1" %)(((
269 +value
270 +)))
271 +|(((
272 +Images number
273 +)))|(((
274 +number of frames you want to collect
275 +)))|(% colspan="1" %)(((
276 +usually 100k - 200k, but adjust according to hitrate
277 +
278 +orientation: 10 % hitrate needs at least 100k images
279 +)))
280 +|(((
281 +exposure
282 +)))|(((
283 +exposure time of Eiger
284 +
285 +
286 +)))|(% colspan="1" %)(((
287 +with chopper         → opening time displayed in chopper GUI
288 +no chopper            → 7.7 ms
289 +
290 +----
291 +)))
292 +|(((
293 +run id
294 +)))|(((
295 +changes automatically
296 +)))|(% colspan="1" %)(((
297 +
298 +)))
299 +|(% colspan="1" %)(((
300 +Detector distance
301 +)))|(% colspan="1" %)(((
302 +current detector postion readout
303 +)))|(% colspan="1" %)(((
304 +
305 +)))
306 +|(% colspan="1" %)(((
307 +protein ID
308 +)))|(% colspan="1" %)(((
309 +protein ID of crystal sample (see AMARCORD)
310 +)))|(% colspan="1" %)(((
311 +
312 +)))
313 +
314 +----
315 +{{/layout-cell}}
316 +{{/layout-section}}
317 +
318 +{{layout-section ac:type="two_equal"}}
319 +{{layout-cell}}
320 +**After data collection/Before entering the exp. hutch:**
321 +
322 +1. Go to "Safety" in kamzik.
323 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
324 +11. Drive the collimator out
325 +11. Drive the detector back to 1500 mm
326 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
327 +
328 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
329 +{{/layout-cell}}
330 +
331 +{{layout-cell}}
332 +
333 +
334 +
335 +
336 +
337 +
338 +[[image:attach:safety_kamzik.PNG]]
339 +{{/layout-cell}}
340 +{{/layout-section}}
341 +
342 +{{layout-section ac:type="single"}}
343 +{{layout-cell}}
344 +----
345 +
346 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**8.7 Troubleshooting** ==
347 +
348 +* (((
349 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
350 +
351 +* Tape roll empty?
352 +* motor connected (icon green)?
353 +)))
354 +
355 +* (((
356 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
357 +
358 +* displayed in green=connected?
359 +* nozzle holder colliding somewhere?
360 +* motor limits reached? → position displayed in red
361 +)))
362 +
363 +* (((
364 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
365 +
366 +* channel turned on?
367 +* Sample empty?
368 +* Nozzle or lines clogged? → flush with water, change nozzle
369 +)))
370 +
371 +* (((
372 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
373 +
374 +* First, restart kamzik (server+client) and see if this solves the issue
375 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
376 +* (((
377 +If nothing works, kill the Simplon process and then start the server again:*
378 +
379 +(((
380 +(% class="code" %)
381 +(((
382 +ssh haspp11exp03
383 +)))
384 +)))
385 +
386 +* (((
387 +(% class="code" %)
388 +(((
389 +ps -ef | grep Simplon
390 +)))
391 +)))
392 +* (((
393 +(% class="code" %)
394 +(((
395 +kill -9 simplon_process_id
396 +)))
397 +)))
398 +)))
399 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
400 +)))
401 +{{/layout-cell}}
402 +{{/layout-section}}
403 +
404 +{{layout-section ac:type="single"}}
405 +{{layout-cell}}
406 +
407 +{{/layout-cell}}
408 +{{/layout-section}}
409 +{{/layout}}
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1 -235031814
1 +235031805
Title
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1 -Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
URL
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1 -https://confluence.desy.de/spaces/11/pages/235031814/Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
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