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Version 36.1 by ahenkel on 2021-12-12 22:53
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3 {{toc/}}
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5 [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
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13 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
14
15 * remove vortex
16 * beamstop to out-position?
17 * remove goniometer. The airbearing should be stopped (p11/servermotor/eh.1.01)
18 * 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.
19 * stop refill of the robot dewar and empty the dewar, warm up.
20 * Disable backlight (unplug Festo connection). (% style="color: rgb(255,0,0);" %)//Is this still needed?//
21 * (% 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.
22 * (% style="color: rgb(0,0,0);" %)move goniotower to X ~~ 17 000
23
24 (% 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.
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26 \\
27
28 * 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).//
29 * (% 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.
30 * (% 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.
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32 \\
33
34 Prepare necessary controls for data collection:
35
36 * ATK panels:
37 ** p11/simplon_filewriter/eh.01
38 ** p11/simplon_detector/eh.01
39 *** count time = 0.0075
40 *** 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.
41 *** numer of images = 100 000
42 *** number of images in container = 1000
43 *** mode 16m/4M
44 *** detector distance = 200 mm (usually)
45 ** p11/detectortower
46 ** p11/motor/eh.09
47 * remote access to TapeDrive control laptop:
48 ** open terminal, execute command:          xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
49 password: //written on control laptop
50 //
51 * Cameras:
52 ** haspp11ethcam1 → detector tower camera to monitor nozzle
53 ** haspp11ethcam4 →  goniometer camera to monitor tape from above
54 * OnDa (on haspp11user04): 
55 //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.//\\
56 ** 16M mode →    cd /home/p11user/CfelSoft/202103_onda
57 ./onda-runner.py onda-config/onda-config-Eiger16M.toml
58 ** 4M mode   →    cd /home/p11user/CfelSoft/202103_onda
59 ./onda-runner.py onda-config/onda-config-Eiger4M.toml\\
60
61 \\
62
63 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 Sample characteristics and preparation** ===
64
65 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.
66
67 Preparation:
68
69 * filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
70
71 [[image:attach:20211201_095534.jpg||height="250"]]
72
73 \\
74
75 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
76 ** ===
77
78 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!**
79
80 Be aware to which channel and nozzle line your sample is connected.
81
82 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
83
84 Green → Channel 2, substrate line (nozzle capillary is marked in black)
85
86 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
87
88 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
89
90 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
91
92 \\
93
94 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
95 ** ===
96
97 The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
98 Now start the client. Same thing, a terminal will open, shortly after a small window.
99
100 Click 'Devices' in the **client session** to open the control window.
101 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
102
103 **Tape**
104
105 * Click on the 'main tape' icon
106 * Change the velocity by typing anything from **0.3-3.0 mm/s**
107 * Common velocity is 1.0-1.5 mm/s
108 * 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.
109 \\
110 * [[image:attach:kamzik_tape.PNG||height="400"]]
111
112 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
113
114 * Click an the 'nozzle' icon.
115 * (((
116 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.
117 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
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119
120 (% 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);" %)** !!!**(%%)
121 \\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.
122
123 (% class="wrapped" %)
124 |=(((
125 \\
126 )))|=(((
127 direction
128 )))|=(((
129 recommended step size
130 for visual adjustment
131 )))|=(% colspan="1" %)(((
132 recommended step size
133 during data collection
134 )))
135 |(((
136 +x
137 )))|(((
138 away from X-ray interaction point
139 )))|(((
140 1.0 - 0.5 mm
141 )))|(% colspan="1" %)(((
142 0.1 - 0.2 mm
143 )))
144 |(((
145 +y
146 )))|(((
147 up
148 )))|(((
149 1.0 - 0.5 mm
150 )))|(% colspan="1" %)(((
151 0.1 - 0.2 mm
152 )))
153 |(((
154 +z
155 )))|(((
156 towards detector tower, away from tape
157 )))|(((
158 0.5 - 0.2 mm
159 )))|(% colspan="1" %)(((
160 0.1 - 0.2 mm
161 be careful with -z, tape could be pushed out of focus
162 )))
163
164 **
165 \\**
166 )))
167 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
168
169 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
170
171 * The chiller circulates fluid through the gas nozzle.
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174
175 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
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178
179 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
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182
183 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
184
185 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
186 password: //written on control laptop (changes every 6 months)
187 //
188
189 \\
190
191 \\
192
193 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
194
195 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).
196
197 * Remove the (almost) empty feeder roll by pulling it upwards.
198 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
199 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
200 * Cut the first cm of the new tape roll, directly behind the black sticky part.
201 * 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.
202 * Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
203 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
204 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
205 * Attach new tape to the empty roll by using some sticky tape.
206 * Close tape stabilizer.
207 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
208
209 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
210 **
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215
216 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
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219
220 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Datacollection"/}}**14.7 Data collection** ===
221
222 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
223
224 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
225 password: //written on control laptop (changes every 6 months)//
226
227 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
228
229 \\
230
231 **Check list:**
232
233 * Open BS1  (//CrystalControl)//
234 * Put collimator in (//CrystalControl)//
235 * Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
236 * Open fast shutter (//CrystalControl)//
237 * Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
238 * Close fast shutter (//CrystalControl)//
239
240 \\
241
242 **Start run in kamzik
243 **
244
245 Click "Start" icon in kamzik.
246
247 [[image:attach:kamzik_run-tile.jpg||height="400"]]
248
249 |=(((
250 Parameter
251 )))|=(((
252 explanation
253 )))|=(% colspan="1" %)(((
254 value
255 )))
256 |(((
257 Images number
258 )))|(((
259 Set number of frames you want to collect
260 )))|(% colspan="1" %)(((
261 usually 100k - 200k, but adjust according to hitrate
262
263 orientation: 10 % hitrate needs at least 100k images
264 )))
265 |(((
266 exposure
267 )))|(((
268 exposure time of Eiger
269
270 \\
271 )))|(% colspan="1" %)(((
272 chopper at 133 Hz → 3.7 ms
273
274 chopper at 66 Hz   → 7.7 ms
275
276 no chopper            → 7.7 ms
277
278 ----
279 )))
280 |(((
281 run id
282 )))|(((
283 changes automatically
284 )))|(% colspan="1" %)(((
285 \\
286 )))
287 |(% colspan="1" %)(((
288 Detector distance
289 )))|(% colspan="1" %)(((
290 current detector postion readout
291 )))|(% colspan="1" %)(((
292 \\
293 )))
294 |(% colspan="1" %)(((
295 move_detector (distance)
296 )))|(% colspan="1" %)(((
297 Set detector distance
298 )))|(% colspan="1" %)(((
299 200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
300 )))
301 |(% colspan="1" %)(((
302 Diode voltage
303 )))|(% colspan="1" %)(((
304 read out of diode
305 )))|(% colspan="1" %)(((
306 **~~ 0 !!! higher values indicate missaligned beam stop!!!**
307 )))
308
309 ----
310
311 (% class="task-list" %)
312 (((
313 {{task reference="/Tasks/Task_6" status="InProgress"}}
314 Set your desired No. of frames
315 {{/task}}
316
317 {{task reference="/Tasks/Task_7" status="InProgress"}}
318 Match exposure time with chopper setting
319 {{/task}}
320
321 {{task reference="/Tasks/Task_8" status="InProgress"}}
322 Check trigger setting and match to chopper setting
323 {{/task}}
324
325 {{task reference="/Tasks/Task_9" status="InProgress"}}
326 Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
327 {{/task}}
328
329 {{task reference="/Tasks/Task_10" status="InProgress"}}
330 To start the run, click "<Call>" next to //exposure time//
331 {{/task}}
332 )))
333
334 ----
335
336 \\
337
338 \\
339
340 === {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Troubleshooting"/}}14.8 Troubleshooting ===
341
342 * (((
343 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
344 )))
345 * (((
346 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
347 )))
348 * (((
349 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
350 )))
351
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