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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.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"/}}**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 +https://confluence.desy.de/spaces/11/pages/235032181/14. Serial Crystallography: CFEL TapeDrive
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