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Version 43.1 by ahenkel on 2021-12-12 23:49
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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 \\
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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 |=(((
123 \\
124 )))|=(((
125 direction
126 )))|=(((
127 recommended step size
128 for visual adjustment
129 )))|=(% colspan="1" %)(((
130 recommended step size
131 during data collection
132 )))
133 |(((
134 +x
135 )))|(((
136 away from X-ray interaction point
137 )))|(((
138 1.0 - 0.5 mm
139 )))|(% colspan="1" %)(((
140 0.1 - 0.2 mm
141 )))
142 |(((
143 +y
144 )))|(((
145 up
146 )))|(((
147 1.0 - 0.5 mm
148 )))|(% colspan="1" %)(((
149 0.1 - 0.2 mm
150 )))
151 |(((
152 +z
153 )))|(((
154 towards detector tower, away from tape
155 )))|(((
156 0.5 - 0.2 mm
157 )))|(% colspan="1" %)(((
158 0.1 - 0.2 mm
159 be careful with -z, tape could be pushed out of focus
160 )))
161
162 **
163 \\**
164 )))
165 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
166
167 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
168
169 * The chiller circulates fluid through the gas nozzle.
170
171 \\
172
173 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
174
175 \\
176
177 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
178
179 \\
180
181 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
182
183 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
184 password: //written on control laptop (changes every 6 months)
185 //
186
187 \\
188
189 \\
190
191 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
192
193 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).
194
195 * Remove the (almost) empty feeder roll by pulling it upwards.
196 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
197 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
198 * Cut the first cm of the new tape roll, directly behind the black sticky part.
199 * 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.
200 * Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
201 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
202 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
203 * Attach new tape to the empty roll by using some sticky tape.
204 * Close tape stabilizer.
205 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
206
207 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
208 **
209
210 \\
211
212 \\
213
214 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
215 {{/layout-cell}}
216 {{/layout-section}}
217
218 {{layout-section ac:type="single"}}
219 {{layout-cell}}
220 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ===
221
222 start chopper gui from terminal:
223
224 (% class="code" %)
225 (((
226 cd /gpfs/local/shared/ChopperControl
227 )))
228
229 (% class="code" %)
230 (((
231 python chopperControl.py
232 )))
233 {{/layout-cell}}
234 {{/layout-section}}
235
236 {{layout-section ac:type="two_equal"}}
237 {{layout-cell}}
238 [[image:attach:20211212_233140.jpg||height="250"]]
239 {{/layout-cell}}
240
241 {{layout-cell}}
242 **Chopper → no Chopper**
243
244 * decrease frequency by max. 10 Hz steps\\
245 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
246 * at frequency = 10 Hz, click "Stop"
247 * set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
248
249 (% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
250
251 * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
252 * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
253 ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
254 * (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
255 {{/layout-cell}}
256 {{/layout-section}}
257
258 {{layout-section ac:type="single"}}
259 {{layout-cell}}
260 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ===
261
262 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
263
264 (% class="code" %)
265 (((
266 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
267 password: written on control laptop (changes every 6 months)
268 )))
269
270 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
271
272 \\
273
274 Click "Start" icon in kamzik.
275
276 [[image:attach:kamzik_run-tile.jpg||height="400"]]
277
278 ----
279 {{/layout-cell}}
280 {{/layout-section}}
281
282 {{layout-section ac:type="two_equal"}}
283 {{layout-cell}}
284 **Check list:**
285
286 (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
287
288 * Open BS1  (//CrystalControl)//
289 * Put collimator in (//CrystalControl)//
290 * Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
291 * Open fast shutter (//CrystalControl)//
292 * Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
293 * Close fast shutter (//CrystalControl)//
294
295 \\
296
297 **Set run parameters and go 🏃💥**
298
299 1. Set your desired No. of frames
300 1. Match exposure time with chopper setting
301 1. Check trigger setting and match to chopper setting
302 1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
303 1. To start the run, click "<Call>" next to //exposure time//
304
305 \\
306
307 (% style="color: rgb(153,51,102);" %)**//Current bug~://**
308
309 (% 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>".
310
311
312 (% style="color: rgb(0,0,0);" %)Check progress in terminal with:
313
314 (% class="code" %)
315 (((
316 cd /gpfs/current/raw/scan_frames
317 watch "ls -lrt <run number>/ | tail"
318 \\\\\\\\
319 )))
320 {{/layout-cell}}
321
322 {{layout-cell}}
323 (% class="wrapped relative-table" style="width: 100.0%;" %)
324 |=(((
325 Parameter
326 )))|=(((
327 explanation
328 )))|=(% colspan="1" %)(((
329 value
330 )))
331 |(((
332 Images number
333 )))|(((
334 Set number of frames you want to collect
335 )))|(% colspan="1" %)(((
336 usually 100k - 200k, but adjust according to hitrate
337
338 orientation: 10 % hitrate needs at least 100k images
339 )))
340 |(((
341 exposure
342 )))|(((
343 exposure time of Eiger
344
345 \\
346 )))|(% colspan="1" %)(((
347 chopper at 133 Hz → 3.7 ms
348
349 chopper at 66 Hz   → 7.7 ms
350
351 no chopper            → 7.7 ms
352
353 ----
354 )))
355 |(((
356 run id
357 )))|(((
358 changes automatically
359 )))|(% colspan="1" %)(((
360 \\
361 )))
362 |(% colspan="1" %)(((
363 Detector distance
364 )))|(% colspan="1" %)(((
365 current detector postion readout
366 )))|(% colspan="1" %)(((
367 \\
368 )))
369 |(% colspan="1" %)(((
370 move_detector (distance)
371 )))|(% colspan="1" %)(((
372 Set detector distance
373 )))|(% colspan="1" %)(((
374 200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
375 )))
376 |(% colspan="1" %)(((
377 Diode voltage
378 )))|(% colspan="1" %)(((
379 read out of diode
380 )))|(% colspan="1" %)(((
381 **~~ 0 !!! higher values indicate missaligned beam stop!!! 
382 Call local contact
383 **
384 )))
385 {{/layout-cell}}
386 {{/layout-section}}
387
388 {{layout-section ac:type="single"}}
389 {{layout-cell}}
390 ----
391
392 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}14.9 Troubleshooting ===
393
394 * (((
395 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
396
397 * Tape roll empty?
398 * motor connected (icon green)?
399 )))
400
401 \\
402
403 * (((
404 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
405
406 * displayed in green=connected?
407 * nozzle holder colliding somewhere?
408 * motor limits reached? → position displayed in red
409 )))
410
411 \\
412
413 * (((
414 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
415
416 * channel turned on?
417 * Sample empty?
418 * Nozzle or lines clogged? → flush with water, change nozzle
419 )))
420 {{/layout-cell}}
421 {{/layout-section}}
422 {{/layout}}