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Version 42.1 by ahenkel on 2021-12-12 23:47
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6 {{toc/}}
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8 [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
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15
16 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
17
18 * remove vortex
19 * beamstop to out-position?
20 * remove goniometer. The airbearing should be stopped (p11/servermotor/eh.1.01)
21 * 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.
22 * stop refill of the robot dewar and empty the dewar, warm up.
23 * Disable backlight (unplug Festo connection). (% style="color: rgb(255,0,0);" %)//Is this still needed?//
24 * (% 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.
25 * (% style="color: rgb(0,0,0);" %)move goniotower to X ~~ 17 000
26
27 (% 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.
28
29 \\
30
31 * 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).//
32 * (% 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.
33 * (% 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.
34
35 \\
36
37 Prepare necessary controls for data collection:
38
39 * ATK panels:
40 ** p11/simplon_filewriter/eh.01
41 ** p11/simplon_detector/eh.01
42 *** count time = 0.0075
43 *** 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.
44 *** numer of images = 100 000
45 *** number of images in container = 1000
46 *** mode 16m/4M
47 *** detector distance = 200 mm (usually)
48 ** p11/detectortower
49 ** p11/motor/eh.09
50 * remote access to TapeDrive control laptop:
51 ** open terminal, execute command:          xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
52 password: //written on control laptop
53 //
54 * Cameras:
55 ** haspp11ethcam1 → detector tower camera to monitor nozzle
56 ** haspp11ethcam4 →  goniometer camera to monitor tape from above
57 * OnDa (on haspp11user04): 
58 //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.//\\
59 ** 16M mode →    cd /home/p11user/CfelSoft/202103_onda
60 ./onda-runner.py onda-config/onda-config-Eiger16M.toml
61 ** 4M mode   →    cd /home/p11user/CfelSoft/202103_onda
62 ./onda-runner.py onda-config/onda-config-Eiger4M.toml\\
63
64 \\
65
66 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 Sample characteristics and preparation** ===
67
68 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.
69
70 Preparation:
71
72 * filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
73
74 [[image:attach:20211201_095534.jpg||height="250"]]
75
76 \\
77
78 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
79 ** ===
80
81 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!**
82
83 Be aware to which channel and nozzle line your sample is connected.
84
85 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
86
87 Green → Channel 2, substrate line (nozzle capillary is marked in black)
88
89 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
90
91 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
92
93 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
94
95 \\
96
97 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
98 ** ===
99
100 The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
101 Now start the client. Same thing, a terminal will open, shortly after a small window.
102
103 Click 'Devices' in the **client session** to open the control window.
104 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
105
106 **Tape**
107
108 * Click on the 'main tape' icon
109 * Change the velocity by typing anything from **0.3-3.0 mm/s**
110 * Common velocity is 1.0-1.5 mm/s
111 * 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.
112 \\
113 * [[image:attach:kamzik_tape.PNG||height="400"]]
114
115 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
116
117 * Click an the 'nozzle' icon.
118 * (((
119 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.
120 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
121
122
123 (% 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);" %)** !!!**(%%)
124 \\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.
125
126 (% class="wrapped" %)
127 |=(((
128 \\
129 )))|=(((
130 direction
131 )))|=(((
132 recommended step size
133 for visual adjustment
134 )))|=(% colspan="1" %)(((
135 recommended step size
136 during data collection
137 )))
138 |(((
139 +x
140 )))|(((
141 away from X-ray interaction point
142 )))|(((
143 1.0 - 0.5 mm
144 )))|(% colspan="1" %)(((
145 0.1 - 0.2 mm
146 )))
147 |(((
148 +y
149 )))|(((
150 up
151 )))|(((
152 1.0 - 0.5 mm
153 )))|(% colspan="1" %)(((
154 0.1 - 0.2 mm
155 )))
156 |(((
157 +z
158 )))|(((
159 towards detector tower, away from tape
160 )))|(((
161 0.5 - 0.2 mm
162 )))|(% colspan="1" %)(((
163 0.1 - 0.2 mm
164 be careful with -z, tape could be pushed out of focus
165 )))
166
167 **
168 \\**
169 )))
170 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
171
172 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
173
174 * The chiller circulates fluid through the gas nozzle.
175
176 \\
177
178 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
179
180 \\
181
182 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
183
184 \\
185
186 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
187
188 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
189 password: //written on control laptop (changes every 6 months)
190 //
191
192 \\
193
194 \\
195
196 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
197
198 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).
199
200 * Remove the (almost) empty feeder roll by pulling it upwards.
201 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
202 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
203 * Cut the first cm of the new tape roll, directly behind the black sticky part.
204 * 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.
205 * Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
206 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
207 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
208 * Attach new tape to the empty roll by using some sticky tape.
209 * Close tape stabilizer.
210 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
211
212 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
213 **
214
215 \\
216
217 \\
218
219 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
220
221 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ===
222
223 start chopper gui from terminal:
224
225 (% class="code" %)
226 (((
227 cd /gpfs/local/shared/ChopperControl
228 )))
229
230 (% class="code" %)
231 (((
232 python chopperControl.py
233 )))
234
235 ----
236 {{/layout-cell}}
237 {{/layout-section}}
238
239 {{layout-section ac:type="two_equal"}}
240 {{layout-cell}}
241 [[image:attach:20211212_233140.jpg||height="250"]]
242 {{/layout-cell}}
243
244 {{layout-cell}}
245 **Chopper → no Chopper**
246
247 * decrease frequency by max. 10 Hz steps\\
248 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
249 * at frequency = 10 Hz, click "Stop"
250 * set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
251
252 (% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
253
254 * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
255 * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
256 ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
257 * (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
258 {{/layout-cell}}
259 {{/layout-section}}
260
261 {{layout-section ac:type="single"}}
262 {{layout-cell}}
263 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ===
264
265 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
266
267 (% class="code" %)
268 (((
269 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
270 password: written on control laptop (changes every 6 months)
271 )))
272
273 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
274
275 \\
276
277 Click "Start" icon in kamzik.
278
279 [[image:attach:kamzik_run-tile.jpg||height="400"]]
280
281 ----
282 {{/layout-cell}}
283 {{/layout-section}}
284
285 {{layout-section ac:type="two_equal"}}
286 {{layout-cell}}
287 **Check list:**
288
289 (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
290
291 * Open BS1  (//CrystalControl)//
292 * Put collimator in (//CrystalControl)//
293 * Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
294 * Open fast shutter (//CrystalControl)//
295 * Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
296 * Close fast shutter (//CrystalControl)//
297
298 \\
299
300 **Set run parameters and go 🏃💥**
301
302 1. Set your desired No. of frames
303 1. Match exposure time with chopper setting
304 1. Check trigger setting and match to chopper setting
305 1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
306 1. To start the run, click "<Call>" next to //exposure time//
307
308 \\
309
310 (% style="color: rgb(153,51,102);" %)**//Current bug~://**
311
312 (% 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>".
313
314
315 (% style="color: rgb(0,0,0);" %)Check progress in terminal with:
316
317 (% class="code" %)
318 (((
319 cd /gpfs/current/raw/scan_frames
320 watch "ls -lrt <run number>/ | tail"
321 \\\\\\\\
322 )))
323 {{/layout-cell}}
324
325 {{layout-cell}}
326 (% class="wrapped relative-table" style="width: 100.0%;" %)
327 |=(((
328 Parameter
329 )))|=(((
330 explanation
331 )))|=(% colspan="1" %)(((
332 value
333 )))
334 |(((
335 Images number
336 )))|(((
337 Set number of frames you want to collect
338 )))|(% colspan="1" %)(((
339 usually 100k - 200k, but adjust according to hitrate
340
341 orientation: 10 % hitrate needs at least 100k images
342 )))
343 |(((
344 exposure
345 )))|(((
346 exposure time of Eiger
347
348 \\
349 )))|(% colspan="1" %)(((
350 chopper at 133 Hz → 3.7 ms
351
352 chopper at 66 Hz   → 7.7 ms
353
354 no chopper            → 7.7 ms
355
356 ----
357 )))
358 |(((
359 run id
360 )))|(((
361 changes automatically
362 )))|(% colspan="1" %)(((
363 \\
364 )))
365 |(% colspan="1" %)(((
366 Detector distance
367 )))|(% colspan="1" %)(((
368 current detector postion readout
369 )))|(% colspan="1" %)(((
370 \\
371 )))
372 |(% colspan="1" %)(((
373 move_detector (distance)
374 )))|(% colspan="1" %)(((
375 Set detector distance
376 )))|(% colspan="1" %)(((
377 200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
378 )))
379 |(% colspan="1" %)(((
380 Diode voltage
381 )))|(% colspan="1" %)(((
382 read out of diode
383 )))|(% colspan="1" %)(((
384 **~~ 0 !!! higher values indicate missaligned beam stop!!! 
385 Call local contact
386 **
387 )))
388 {{/layout-cell}}
389 {{/layout-section}}
390
391 {{layout-section ac:type="single"}}
392 {{layout-cell}}
393 ----
394
395 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}14.9 Troubleshooting ===
396
397 * (((
398 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
399
400 * Tape roll empty?
401 * motor connected (icon green)?
402 )))
403
404 \\
405
406 * (((
407 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
408
409 * displayed in green=connected?
410 * nozzle holder colliding somewhere?
411 * motor limits reached? → position displayed in red
412 )))
413
414 \\
415
416 * (((
417 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
418
419 * channel turned on?
420 * Sample empty?
421 * Nozzle or lines clogged? → flush with water, change nozzle
422 )))
423 {{/layout-cell}}
424 {{/layout-section}}
425 {{/layout}}