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Version 44.1 by ahenkel on 2021-12-12 23:50
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1 {{layout}}
2 {{layout-section ac:type="single"}}
3 {{layout-cell}}
4 [[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
5
6 \\
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8 \\
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10 \\
11
12 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
13
14 * remove vortex
15 * beamstop to out-position?
16 * remove goniometer. The airbearing should be stopped (p11/servermotor/eh.1.01)
17 * move cryojet out of the way, ramp the cryo up and shut it down. Close the compressed air to the shield flow. The biggest cable kinks and needs to be disconnected.
18 * stop refill of the robot dewar and empty the dewar, warm up.
19 * Disable backlight (unplug Festo connection). (% style="color: rgb(255,0,0);" %)//Is this still needed?//
20 * (% style="color: rgb(0,0,0);" %)mount the 10 um diode and connect (via connector on the granite). This is connected to the leftmost Keithly (power up, check that settings are gain E06, Filter on, Rise time 1 ms. Keithly is connected to the oscilloscope and the delay generator, delay generator is connected to oscilloscope and detector, see diagram in P11 wiki. (% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)//Insert here the setting for oscilloscope//(% style="color: rgb(0,0,0);" %)//. //Make sure to connect the multi-trigger to the back of the detector instead of the standard trigger, when starting to use the chopper (pull the thin ring with ‘grip’ area to detach). Cables are labeled. Make sure before using the chopper that the channels are enabled.
21 * (% style="color: rgb(0,0,0);" %)move goniotower to X ~~ 17 000
22
23 (% style="color: rgb(0,0,0);" %)Mounting of the TapeDrive is done by the CFEL group. Electronics and control units are combined on a small shelf, that requires only one power and network plug-in. The shelf will be placed left-sided (looking upstream) to the detector tower. The ElveFlow and control laptop as well as several necessary consumables are placed on a cart, which is to be positioned on the right (looking upstream) against the robot platform. The CFEL chiller is placed on the right of the platform and connected to the TapeDrive GASnozzle.
24
25 \\
26
27 * adjust focus of the tape by moving X in goniometer tower until you see it in the overview camera. Final adjustment should be done when there is flow. Latest value is about 4500 in X and also 5000 in Z (higher soft limit changed from 2976,63 to 6000). (% style="color: rgb(255,0,0);" %)//Better to use the back illumination in the GUI to focus the tape - old instruction, not sure if this is the case. Back illumination is the external light source in the detector tower (the crystallography backlight should be disable for tapedrive).//
28 * (% style="color: rgb(0,0,0);" %)Check the Minimum Detector Distance; the detector should not collide with the tapedrive while driven to 154 mm but it has to be verified. Also check that all cables and capillaries are taped away when the users start, so that nothing protrudes further than the tapedrive itself. Soft limit can be edited in eh.3.11 Atk panel.
29 * (% style="color: rgb(0,0,0);" %)Reconfirm the alignment of the beamstop, once everything, including the nozzle, is in place. Modify config.ini for beamstop in- and out-position to both mach in (27 000). This way the beamstop will not be driven out when the hutch is opened, to avoid that the users forget to drive it in when restarting after entering the hutch.
30
31 \\
32
33 Prepare necessary controls for data collection:
34
35 * ATK panels:
36 ** p11/simplon_filewriter/eh.01
37 ** p11/simplon_detector/eh.01
38 *** count time = 0.0075
39 *** trigger (**ints **if working without the chopper, # or triggers is 1, **exts** if with the chopper, # or triggers = number of images). Exts is also the standard trigger in normal crystallography. If GUI is used to take images (e.g. for beamstop alignment) the trigger mode will be forced by that and needs to be reverted manually for the users to continue.
40 *** numer of images = 100 000
41 *** number of images in container = 1000
42 *** mode 16m/4M
43 *** detector distance = 200 mm (usually)
44 ** p11/detectortower
45 ** p11/motor/eh.09
46 * remote access to TapeDrive control laptop:
47 ** open terminal, execute command:          xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
48 password: //written on control laptop
49 //
50 * Cameras:
51 ** haspp11ethcam1 → detector tower camera to monitor nozzle
52 ** haspp11ethcam4 →  goniometer camera to monitor tape from above
53 * OnDa (on haspp11user04): 
54 //This starts both GUIs (Frame Viewer & Crystallography GUI) and onda-monitor, the server component. The tool has a bunch of parameters which you can list with ./onda-runner.py —help.//\\
55 ** 16M mode →    cd /home/p11user/CfelSoft/202103_onda
56 ./onda-runner.py onda-config/onda-config-Eiger16M.toml
57 ** 4M mode   →    cd /home/p11user/CfelSoft/202103_onda
58 ./onda-runner.py onda-config/onda-config-Eiger4M.toml\\
59
60 \\
61
62 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 Sample characteristics and preparation** ===
63
64 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.
65
66 Preparation:
67
68 * filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
69
70 [[image:attach:20211201_095534.jpg||height="250"]]
71
72 \\
73
74 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
75 ** ===
76
77 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!**
78
79 Be aware to which channel and nozzle line your sample is connected.
80
81 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
82
83 Green → Channel 2, substrate line (nozzle capillary is marked in black)
84
85 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
86
87 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
88
89 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
90
91 \\
92
93 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
94 ** ===
95
96 The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
97 Now start the client. Same thing, a terminal will open, shortly after a small window.
98
99 Click 'Devices' in the **client session** to open the control window.
100 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
101
102 **Tape**
103
104 * Click on the 'main tape' icon
105 * Change the velocity by typing anything from **0.3-3.0 mm/s**
106 * Common velocity is 1.0-1.5 mm/s
107 * 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.
108 \\
109 * [[image:attach:kamzik_tape.PNG||height="400"]]
110
111 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
112
113 * Click an the 'nozzle' icon.
114 * (((
115 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.
116 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
117
118
119 (% 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);" %)** !!!**(%%)
120 \\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.
121
122 (% class="wrapped" %)
123 |=(((
124 \\
125 )))|=(((
126 direction
127 )))|=(((
128 recommended step size
129 for visual adjustment
130 )))|=(% colspan="1" %)(((
131 recommended step size
132 during data collection
133 )))
134 |(((
135 +x
136 )))|(((
137 away from X-ray interaction point
138 )))|(((
139 1.0 - 0.5 mm
140 )))|(% colspan="1" %)(((
141 0.1 - 0.2 mm
142 )))
143 |(((
144 +y
145 )))|(((
146 up
147 )))|(((
148 1.0 - 0.5 mm
149 )))|(% colspan="1" %)(((
150 0.1 - 0.2 mm
151 )))
152 |(((
153 +z
154 )))|(((
155 towards detector tower, away from tape
156 )))|(((
157 0.5 - 0.2 mm
158 )))|(% colspan="1" %)(((
159 0.1 - 0.2 mm
160 be careful with -z, tape could be pushed out of focus
161 )))
162
163 **
164 \\**
165 )))
166 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
167
168 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
169
170 * The chiller circulates fluid through the gas nozzle.
171
172 \\
173
174 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
175
176 \\
177
178 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
179
180 \\
181
182 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
183
184 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
185 password: //written on control laptop (changes every 6 months)
186 //
187
188 \\
189
190 \\
191
192 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
193
194 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).
195
196 * Remove the (almost) empty feeder roll by pulling it upwards.
197 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
198 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
199 * Cut the first cm of the new tape roll, directly behind the black sticky part.
200 * 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.
201 * Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
202 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
203 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
204 * Attach new tape to the empty roll by using some sticky tape.
205 * Close tape stabilizer.
206 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
207
208 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
209 **
210
211 \\
212
213 \\
214
215 === {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
216 ** ===
217 {{/layout-cell}}
218 {{/layout-section}}
219
220 {{layout-section ac:type="single"}}
221 {{layout-cell}}
222 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ===
223
224 start chopper gui from terminal:
225
226 (% class="code" %)
227 (((
228 cd /gpfs/local/shared/ChopperControl
229 )))
230
231 (% class="code" %)
232 (((
233 python chopperControl.py
234 )))
235 {{/layout-cell}}
236 {{/layout-section}}
237
238 {{layout-section ac:type="two_equal"}}
239 {{layout-cell}}
240 [[image:attach:20211212_233140.jpg||height="250"]]
241 {{/layout-cell}}
242
243 {{layout-cell}}
244 **Chopper → no Chopper**
245
246 * decrease frequency by max. 10 Hz steps\\
247 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
248 * at frequency = 10 Hz, click "Stop"
249 * set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
250
251 (% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
252
253 * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
254 * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
255 ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
256 * (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
257 {{/layout-cell}}
258 {{/layout-section}}
259
260 {{layout-section ac:type="single"}}
261 {{layout-cell}}
262 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ===
263
264 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
265
266 (% class="code" %)
267 (((
268 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
269 password: written on control laptop (changes every 6 months)
270 )))
271
272 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
273
274 \\
275
276 Click "Start" icon in kamzik.
277
278 [[image:attach:kamzik_run-tile.jpg||height="400"]]
279
280 ----
281 {{/layout-cell}}
282 {{/layout-section}}
283
284 {{layout-section ac:type="two_equal"}}
285 {{layout-cell}}
286 **Check list:**
287
288 (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
289
290 * Open BS1  (//CrystalControl)//
291 * Put collimator in (//CrystalControl)//
292 * Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
293 * Open fast shutter (//CrystalControl)//
294 * Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
295 * Close fast shutter (//CrystalControl)//
296
297 \\
298
299 **Set run parameters and go 🏃💥**
300
301 1. Set your desired No. of frames
302 1. Match exposure time with chopper setting
303 1. Check trigger setting and match to chopper setting
304 1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
305 1. To start the run, click "<Call>" next to //exposure time//
306
307 \\
308
309 (% style="color: rgb(153,51,102);" %)**//Current bug~://**
310
311 (% style="color: rgb(0,0,0);" %)You need to "Stop" run in kamzik manually after all images have been acquired. This moves the shield up and closes the fast shutter. Afterwards you can start a new run by clicking "<Call>".
312
313
314 (% style="color: rgb(0,0,0);" %)Check progress in terminal with:
315
316 (% class="code" %)
317 (((
318 cd /gpfs/current/raw/scan_frames
319 watch "ls -lrt <run number>/ | tail"
320 \\\\\\\\
321 )))
322 {{/layout-cell}}
323
324 {{layout-cell}}
325 (% class="wrapped relative-table" style="width: 100.0%;" %)
326 |=(((
327 Parameter
328 )))|=(((
329 explanation
330 )))|=(% colspan="1" %)(((
331 value
332 )))
333 |(((
334 Images number
335 )))|(((
336 Set number of frames you want to collect
337 )))|(% colspan="1" %)(((
338 usually 100k - 200k, but adjust according to hitrate
339
340 orientation: 10 % hitrate needs at least 100k images
341 )))
342 |(((
343 exposure
344 )))|(((
345 exposure time of Eiger
346
347 \\
348 )))|(% colspan="1" %)(((
349 chopper at 133 Hz → 3.7 ms
350
351 chopper at 66 Hz   → 7.7 ms
352
353 no chopper            → 7.7 ms
354
355 ----
356 )))
357 |(((
358 run id
359 )))|(((
360 changes automatically
361 )))|(% colspan="1" %)(((
362 \\
363 )))
364 |(% colspan="1" %)(((
365 Detector distance
366 )))|(% colspan="1" %)(((
367 current detector postion readout
368 )))|(% colspan="1" %)(((
369 \\
370 )))
371 |(% colspan="1" %)(((
372 move_detector (distance)
373 )))|(% colspan="1" %)(((
374 Set detector distance
375 )))|(% colspan="1" %)(((
376 200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
377 )))
378 |(% colspan="1" %)(((
379 Diode voltage
380 )))|(% colspan="1" %)(((
381 read out of diode
382 )))|(% colspan="1" %)(((
383 **~~ 0 !!! higher values indicate missaligned beam stop!!! 
384 Call local contact
385 **
386 )))
387 {{/layout-cell}}
388 {{/layout-section}}
389
390 {{layout-section ac:type="single"}}
391 {{layout-cell}}
392 ----
393
394 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}14.9 Troubleshooting ===
395
396 * (((
397 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
398
399 * Tape roll empty?
400 * motor connected (icon green)?
401 )))
402
403 \\
404
405 * (((
406 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
407
408 * displayed in green=connected?
409 * nozzle holder colliding somewhere?
410 * motor limits reached? → position displayed in red
411 )))
412
413 \\
414
415 * (((
416 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
417
418 * channel turned on?
419 * Sample empty?
420 * Nozzle or lines clogged? → flush with water, change nozzle
421 )))
422 {{/layout-cell}}
423 {{/layout-section}}
424 {{/layout}}