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Version 45.1 by ahenkel on 2021-12-12 23:53
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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 \\
7
8 \\
9
10 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
11
12 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.
13
14 Preparation:
15
16 * filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
17
18 [[image:attach:20211201_095534.jpg||height="250"]]
19
20 \\
21
22 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
23 ** ==
24
25 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!**
26
27 Be aware to which channel and nozzle line your sample is connected.
28
29 Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
30
31 Green → Channel 2, substrate line (nozzle capillary is marked in black)
32
33 [[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
34
35 After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
36
37 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
38
39 \\
40
41 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
42 ** ==
43
44 The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
45 Now start the client. Same thing, a terminal will open, shortly after a small window.
46
47 Click 'Devices' in the **client session** to open the control window.
48 [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
49
50 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
51
52 * Click on the 'main tape' icon
53 * Change the velocity by typing anything from **0.3-3.0 mm/s**
54 * Common velocity is 1.0-1.5 mm/s
55 * 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.
56 \\
57 * [[image:attach:kamzik_tape.PNG||height="400"]]
58
59 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
60
61 * Click an the 'nozzle' icon.
62 * (((
63 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.
64 The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
65
66
67 (% 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);" %)** !!!**(%%)
68 \\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.
69
70 (% class="wrapped" %)
71 |=(((
72 \\
73 )))|=(((
74 direction
75 )))|=(((
76 recommended step size
77 for visual adjustment
78 )))|=(% colspan="1" %)(((
79 recommended step size
80 during data collection
81 )))
82 |(((
83 +x
84 )))|(((
85 away from X-ray interaction point
86 )))|(((
87 1.0 - 0.5 mm
88 )))|(% colspan="1" %)(((
89 0.1 - 0.2 mm
90 )))
91 |(((
92 +y
93 )))|(((
94 up
95 )))|(((
96 1.0 - 0.5 mm
97 )))|(% colspan="1" %)(((
98 0.1 - 0.2 mm
99 )))
100 |(((
101 +z
102 )))|(((
103 towards detector tower, away from tape
104 )))|(((
105 0.5 - 0.2 mm
106 )))|(% colspan="1" %)(((
107 0.1 - 0.2 mm
108 be careful with -z, tape could be pushed out of focus
109 )))
110
111 **
112 \\**
113 )))
114 * [[image:attach:kamzik_nozzle.PNG||height="400"]]
115
116 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
117
118 * The chiller circulates fluid through the gas nozzle.
119
120 \\
121
122 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
123
124 \\
125
126 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
127
128 \\
129
130 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
131
132 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
133 password: //written on control laptop (changes every 6 months)
134 //
135
136 \\
137
138 \\
139
140 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ==
141
142 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).
143
144 * Remove the (almost) empty feeder roll by pulling it upwards.
145 * Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
146 * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
147 * Cut the first cm of the new tape roll, directly behind the black sticky part.
148 * 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.
149 * Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
150 * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
151 * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
152 * Attach new tape to the empty roll by using some sticky tape.
153 * Close tape stabilizer.
154 * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
155
156 **[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
157 **
158
159 \\
160
161 \\
162
163 === {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
164 ** ===
165 {{/layout-cell}}
166 {{/layout-section}}
167
168 {{layout-section ac:type="single"}}
169 {{layout-cell}}
170 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 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 {{/layout-cell}}
184 {{/layout-section}}
185
186 {{layout-section ac:type="two_equal"}}
187 {{layout-cell}}
188 [[image:attach:20211212_233140.jpg||height="250"]]
189 {{/layout-cell}}
190
191 {{layout-cell}}
192 **Chopper → no Chopper**
193
194 * decrease frequency by max. 10 Hz steps\\
195 ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
196 * at frequency = 10 Hz, click "Stop"
197 * set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
198
199 (% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
200
201 * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
202 * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
203 ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
204 * (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
205 {{/layout-cell}}
206 {{/layout-section}}
207
208 {{layout-section ac:type="single"}}
209 {{layout-cell}}
210 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ==
211
212 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
213
214 (% class="code" %)
215 (((
216 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
217 password: written on control laptop (changes every 6 months)
218 )))
219
220 //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
221
222 \\
223
224 Click "Start" icon in kamzik.
225
226 [[image:attach:kamzik_run-tile.jpg||height="400"]]
227
228 ----
229 {{/layout-cell}}
230 {{/layout-section}}
231
232 {{layout-section ac:type="two_equal"}}
233 {{layout-cell}}
234 **Check list:**
235
236 (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
237
238 * Open BS1  (//CrystalControl)//
239 * Put collimator in (//CrystalControl)//
240 * Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
241 * Open fast shutter (//CrystalControl)//
242 * Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
243 * Close fast shutter (//CrystalControl)//
244
245 \\
246
247 **Set run parameters and go 🏃💥**
248
249 1. Set your desired No. of frames
250 1. Match exposure time with chopper setting
251 1. Check trigger setting and match to chopper setting
252 1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
253 1. To start the run, click "<Call>" next to //exposure time//
254
255 \\
256
257 (% style="color: rgb(153,51,102);" %)**//Current bug~://**
258
259 (% 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>".
260
261
262 (% style="color: rgb(0,0,0);" %)Check progress in terminal with:
263
264 (% class="code" %)
265 (((
266 cd /gpfs/current/raw/scan_frames
267 watch "ls -lrt <run number>/ | tail"
268 \\\\\\\\
269 )))
270 {{/layout-cell}}
271
272 {{layout-cell}}
273 (% class="wrapped relative-table" style="width: 100.0%;" %)
274 |=(((
275 Parameter
276 )))|=(((
277 explanation
278 )))|=(% colspan="1" %)(((
279 value
280 )))
281 |(((
282 Images number
283 )))|(((
284 Set number of frames you want to collect
285 )))|(% colspan="1" %)(((
286 usually 100k - 200k, but adjust according to hitrate
287
288 orientation: 10 % hitrate needs at least 100k images
289 )))
290 |(((
291 exposure
292 )))|(((
293 exposure time of Eiger
294
295 \\
296 )))|(% colspan="1" %)(((
297 chopper at 133 Hz → 3.7 ms
298
299 chopper at 66 Hz   → 7.7 ms
300
301 no chopper            → 7.7 ms
302
303 ----
304 )))
305 |(((
306 run id
307 )))|(((
308 changes automatically
309 )))|(% colspan="1" %)(((
310 \\
311 )))
312 |(% colspan="1" %)(((
313 Detector distance
314 )))|(% colspan="1" %)(((
315 current detector postion readout
316 )))|(% colspan="1" %)(((
317 \\
318 )))
319 |(% colspan="1" %)(((
320 move_detector (distance)
321 )))|(% colspan="1" %)(((
322 Set detector distance
323 )))|(% colspan="1" %)(((
324 200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
325 )))
326 |(% colspan="1" %)(((
327 Diode voltage
328 )))|(% colspan="1" %)(((
329 read out of diode
330 )))|(% colspan="1" %)(((
331 **~~ 0 !!! higher values indicate missaligned beam stop!!! 
332 Call local contact
333 **
334 )))
335 {{/layout-cell}}
336 {{/layout-section}}
337
338 {{layout-section ac:type="single"}}
339 {{layout-cell}}
340 ----
341
342 == {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}**14.9 Troubleshooting** ==
343
344 * (((
345 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
346
347 * Tape roll empty?
348 * motor connected (icon green)?
349 )))
350
351 \\
352
353 * (((
354 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
355
356 * displayed in green=connected?
357 * nozzle holder colliding somewhere?
358 * motor limits reached? → position displayed in red
359 )))
360
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 {{/layout-cell}}
371 {{/layout-section}}
372 {{/layout}}