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Last modified by chatzies on 2025-11-27 11:35
From version 83.4
edited by tabermah
on 2024-12-10 15:50
Change comment: There is no comment for this version
To version 74.1
edited by ahenkel
on 2022-05-07 19:08
Change comment: There is no comment for this version

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Title
... ... @@ -1,1 +1,1 @@
1 -08. Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.tabermah
1 +XWiki.ahenkel
Content
... ... @@ -3,28 +3,32 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 -{{toc/}}
8 +{{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 11  
12 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. Sample characteristics and preparation =
14 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
13 13  
14 -* 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.
16 +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.
15 15  
16 16  Preparation:
17 17  
18 -* filter through 30 µm (green) or 50 µm (yellow) cell filter into an Eppendorf or Falcon (original!) tube
20 +* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
19 19  
20 20  [[image:attach:20211201_095534.jpg||height="250"]]
21 21  
24 +\\
22 22  
23 23  ----
24 24  
25 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}8.2. Connecting sample to ElveFlow, sample exchange =
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
26 26  
27 -After filtration, screw the ElveFlow connector to your Eppendorf or Falcon tube. Make sure that the yellow-ish tube goes all the way 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!**
31 +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!**
28 28  
29 29  Be aware to which channel and nozzle line your sample is connected.
30 30  
... ... @@ -38,31 +38,30 @@
38 38  
39 39  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40 40  
45 +\\
41 41  
42 42  ----
43 43  
44 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. TapeDrive operation =
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 +** ==
45 45  
46 -​​​​​​The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
47 -
52 +The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
48 48  Now start the client. Same thing, a terminal will open, shortly after a small window.
49 49  
50 50  Click 'Devices' in the **client session** to open the control window.
51 51  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
52 52  
53 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}Tape ==
58 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
54 54  
55 55  * Click the 'main tape' icon
56 56  * Change the velocity by typing anything from **0.3-3.0 mm/s**
57 57  * Common velocity is 1.0-1.5 mm/s
58 58  * 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.
59 -
64 +\\
65 +* [[image:attach:kamzik_tape.PNG||height="400"]]
60 60  
61 -[[image:attach:kamzik_tape.PNG||height="400"]]
67 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
62 62  
63 -
64 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
65 -
66 66  * Click on the 'nozzle' icon.
67 67  * (((
68 68  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.
... ... @@ -69,16 +69,16 @@
69 69  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
70 70  
71 71  
72 -(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving the nozzle, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
75 +(% 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);" %)** !!!**(%%)
73 73  \\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.
74 74  
75 75  (% class="wrapped" %)
76 76  |=(((
77 -
80 +\\
78 78  )))|=(((
79 79  direction
80 80  )))|=(((
81 -recommended step size
84 +recommended step size
82 82  for visual adjustment
83 83  )))|=(% colspan="1" %)(((
84 84  recommended step size
... ... @@ -113,32 +113,38 @@
113 113  be careful with -z, tape could be pushed out of focus
114 114  )))
115 115  
116 -
119 +**
120 +\\**
117 117  )))
122 +* [[image:attach:kamzik_nozzle.PNG||height="400"]]
118 118  
119 -[[image:attach:kamzik_nozzle.PNG||height="400"]]
124 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
120 120  
121 -
122 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
123 -
124 124  * The chiller circulates fluid through the gas nozzle.
125 125  
126 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
128 +\\
127 127  
130 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
128 128  
129 -== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
132 +\\
130 130  
134 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
131 131  
136 +\\
137 +
132 132  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
133 133  
134 134   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
135 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
136 136  
144 +\\
137 137  
146 +\\
138 138  
139 139  ----
140 140  
141 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
142 142  
143 143  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).
144 144  
... ... @@ -147,7 +147,7 @@
147 147  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
148 148  * Cut the first cm of the new tape roll, directly behind the black sticky part.
149 149  * 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.
150 -* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
151 151  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
152 152  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
153 153  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -154,11 +154,15 @@
154 154  * Close tape stabilizer.
155 155  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
156 156  
157 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
166 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 +**
158 158  
169 +\\
159 159  
171 +\\
160 160  
161 -
173 +**
174 +**
162 162  {{/layout-cell}}
163 163  {{/layout-section}}
164 164  
... ... @@ -166,19 +166,19 @@
166 166  {{layout-cell}}
167 167  ----
168 168  
169 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
170 170  
171 171  start chopper gui from terminal:
172 172  
173 173  (% class="code" %)
174 174  (((
175 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
176 176  )))
177 177  
178 178  (% class="code" %)
179 179  (((
180 180   python chopperControl.py
181 -\\
194 +\\\\
182 182  )))
183 183  {{/layout-cell}}
184 184  {{/layout-section}}
... ... @@ -191,17 +191,18 @@
191 191  {{layout-cell}}
192 192  **Chopper → no Chopper**
193 193  
194 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
195 195  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
196 196  * at frequency = 10 Hz, click "Stop"
197 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
198 198  
199 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
200 200  
201 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
202 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
203 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
204 -* (% style="color:#000000" %)//usually 130 Hz, results in exposure time of 3.7 ms (technical exposure will always be 7.7 ms, since max. frame rate is 130 Hz//
214 +* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
215 +* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
216 +** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
217 +* (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms (technical exposure will always be 7.7 ms, since max. frame rate is 133 Hz
218 +//
205 205  {{/layout-cell}}
206 206  {{/layout-section}}
207 207  
... ... @@ -209,19 +209,19 @@
209 209  {{layout-cell}}
210 210  ----
211 211  
212 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
213 213  
214 214  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
215 215  
216 216  (% class="code" %)
217 217  (((
218 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
232 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
219 219   password: written on control laptop (changes every 6 months)
220 220  )))
221 221  
222 222   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
223 223  
224 -
238 +\\
225 225  {{/layout-cell}}
226 226  {{/layout-section}}
227 227  
... ... @@ -229,26 +229,29 @@
229 229  {{layout-cell}}
230 230  **Check list:**
231 231  
232 -(% style="color:#ff0000" %)//always after entering the hutch!//
246 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
233 233  
234 -(% style="color:#000000" %)Click "Run" icon in kamzik.
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
235 235  
236 -* Put detector distance 200 in //prepare_for_measurement (      )//
237 -* Click "<Call>" next to //prepare_for_measurement//
238 -This will:
239 -** drive the collimator in //IN// position
240 -** drive detector to 200 mm
250 +* Put collimator in
251 +** Put detector distance 200 in //prepare_for_measurement (      )
252 +//
253 +** Click "<Call>" next to //prepare_for_measurement//
241 241  
242 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
255 +\\
243 243  
257 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
258 +
259 +\\
260 +
244 244  //**Set run parameters and go 🏃💥**//
245 245  
246 246  1. Set your desired No. of frames
247 -1. Enter the protein ID of your crystal sample
248 248  1. Match exposure time with chopper setting or set desired exposure time
249 249  1. Check trigger setting and match to chopper setting
250 -no chopper → external triffer //off//
251 - chopper → external trigger// on//
266 +no chopper → external triffer //off
267 +// chopper → external trigger// on
268 +//
252 252  1. To start the run, click "<Call>" next to //start_run (exposure    )//
253 253  {{/layout-cell}}
254 254  
... ... @@ -259,7 +259,7 @@
259 259  
260 260  {{layout-section ac:type="single"}}
261 261  {{layout-cell}}
262 -(% class="relative-table wrapped" style="width:55.9569%" %)
279 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
263 263  |=(((
264 264  Parameter
265 265  )))|=(((
... ... @@ -281,9 +281,12 @@
281 281  )))|(((
282 282  exposure time of Eiger
283 283  
284 -
301 +\\
285 285  )))|(% colspan="1" %)(((
286 -with chopper         → opening time displayed in chopper GUI
303 +chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
304 +
305 +chopper at 66 Hz   → 7.7 ms
306 +
287 287  no chopper            → 7.7 ms
288 288  
289 289  ----
... ... @@ -293,7 +293,7 @@
293 293  )))|(((
294 294  changes automatically
295 295  )))|(% colspan="1" %)(((
296 -
316 +\\
297 297  )))
298 298  |(% colspan="1" %)(((
299 299  Detector distance
... ... @@ -300,15 +300,8 @@
300 300  )))|(% colspan="1" %)(((
301 301  current detector postion readout
302 302  )))|(% colspan="1" %)(((
303 -
323 +\\
304 304  )))
305 -|(% colspan="1" %)(((
306 -protein ID
307 -)))|(% colspan="1" %)(((
308 -protein ID of crystal sample (see AMARCORD)
309 -)))|(% colspan="1" %)(((
310 -
311 -)))
312 312  
313 313  ----
314 314  {{/layout-cell}}
... ... @@ -328,11 +328,15 @@
328 328  {{/layout-cell}}
329 329  
330 330  {{layout-cell}}
331 -
344 +\\
332 332  
346 +\\
333 333  
348 +\\
334 334  
350 +\\
335 335  
352 +\\
336 336  
337 337  [[image:attach:safety_kamzik.PNG]]
338 338  {{/layout-cell}}
... ... @@ -342,17 +342,19 @@
342 342  {{layout-cell}}
343 343  ----
344 344  
345 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
362 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
346 346  
347 347  * (((
348 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
365 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
349 349  
350 350  * Tape roll empty?
351 351  * motor connected (icon green)?
352 352  )))
353 353  
371 +\\
372 +
354 354  * (((
355 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
374 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
356 356  
357 357  * displayed in green=connected?
358 358  * nozzle holder colliding somewhere?
... ... @@ -359,8 +359,10 @@
359 359  * motor limits reached? → position displayed in red
360 360  )))
361 361  
381 +\\
382 +
362 362  * (((
363 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
384 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
364 364  
365 365  * channel turned on?
366 366  * Sample empty?
... ... @@ -367,21 +367,20 @@
367 367  * Nozzle or lines clogged? → flush with water, change nozzle
368 368  )))
369 369  
391 +\\
392 +
370 370  * (((
371 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
394 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
372 372  
373 373  * First, restart kamzik (server+client) and see if this solves the issue
374 374  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
375 375  * (((
376 -If nothing works, kill the Simplon process and then start the server again:*
377 -
378 -(((
399 +If nothing works, kill the Simplon process and then start the server again:* (((
379 379  (% class="code" %)
380 380  (((
381 381  ssh haspp11exp03
382 382  )))
383 383  )))
384 -
385 385  * (((
386 386  (% class="code" %)
387 387  (((
... ... @@ -395,7 +395,6 @@
395 395  )))
396 396  )))
397 397  )))
398 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
399 399  )))
400 400  {{/layout-cell}}
401 401  {{/layout-section}}
... ... @@ -402,7 +402,7 @@
402 402  
403 403  {{layout-section ac:type="single"}}
404 404  {{layout-cell}}
405 -
424 +\\
406 406  {{/layout-cell}}
407 407  {{/layout-section}}
408 408  {{/layout}}
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