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Last modified by chatzies on 2025-11-27 11:35
From version 77.1
edited by tabermah
on 2024-12-03 11:26
Change comment: There is no comment for this version
To version 75.1
edited by ahenkel
on 2022-05-07 20:15
Change comment: There is no comment for this version

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Title
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1 -10. Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.tabermah
1 +XWiki.ahenkel
Content
... ... @@ -3,9 +3,11 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 7  {{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 11  
... ... @@ -19,12 +19,11 @@
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"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26 -
27 -*
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
28 28  ** ==
29 29  
30 30  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!**
... ... @@ -41,15 +41,14 @@
41 41  
42 42  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
43 43  
45 +\\
44 44  
45 45  ----
46 46  
47 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48 -
49 -*
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 50  ** ==
51 51  
52 -The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
52 +The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
53 53  Now start the client. Same thing, a terminal will open, shortly after a small window.
54 54  
55 55  Click 'Devices' in the **client session** to open the control window.
... ... @@ -61,7 +61,7 @@
61 61  * Change the velocity by typing anything from **0.3-3.0 mm/s**
62 62  * Common velocity is 1.0-1.5 mm/s
63 63  * 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.
64 -
64 +\\
65 65  * [[image:attach:kamzik_tape.PNG||height="400"]]
66 66  
67 67  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
... ... @@ -72,16 +72,16 @@
72 72  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
73 73  
74 74  
75 -(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving, 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);" %)** !!!**(%%)
76 76  \\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.
77 77  
78 78  (% class="wrapped" %)
79 79  |=(((
80 -
80 +\\
81 81  )))|=(((
82 82  direction
83 83  )))|=(((
84 -recommended step size
84 +recommended step size
85 85  for visual adjustment
86 86  )))|=(% colspan="1" %)(((
87 87  recommended step size
... ... @@ -116,8 +116,8 @@
116 116  be careful with -z, tape could be pushed out of focus
117 117  )))
118 118  
119 -
120 -
119 +**
120 +\\**
121 121  )))
122 122  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
123 123  
... ... @@ -125,19 +125,25 @@
125 125  
126 126  * The chiller circulates fluid through the gas nozzle.
127 127  
128 +\\
128 128  
129 129  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
130 130  
132 +\\
131 131  
132 132  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
133 133  
136 +\\
134 134  
135 135  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
136 136  
137 137   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
138 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
139 139  
144 +\\
140 140  
146 +\\
141 141  
142 142  ----
143 143  
... ... @@ -150,7 +150,7 @@
150 150  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
151 151  * Cut the first cm of the new tape roll, directly behind the black sticky part.
152 152  * 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.
153 -* 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!!!//
154 154  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
155 155  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
156 156  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -157,11 +157,15 @@
157 157  * Close tape stabilizer.
158 158  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
159 159  
160 -**[[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 +**
161 161  
169 +\\
162 162  
171 +\\
163 163  
164 -
173 +**
174 +**
165 165  {{/layout-cell}}
166 166  {{/layout-section}}
167 167  
... ... @@ -175,13 +175,13 @@
175 175  
176 176  (% class="code" %)
177 177  (((
178 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
179 179  )))
180 180  
181 181  (% class="code" %)
182 182  (((
183 183   python chopperControl.py
184 -\\
194 +\\\\
185 185  )))
186 186  {{/layout-cell}}
187 187  {{/layout-section}}
... ... @@ -194,17 +194,18 @@
194 194  {{layout-cell}}
195 195  **Chopper → no Chopper**
196 196  
197 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
198 198  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
199 199  * at frequency = 10 Hz, click "Stop"
200 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
201 201  
202 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
203 203  
204 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
205 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
206 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
207 -* (% 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 +//
208 208  {{/layout-cell}}
209 209  {{/layout-section}}
210 210  
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218 218  
219 219  (% class="code" %)
220 220  (((
221 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
232 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
222 222   password: written on control laptop (changes every 6 months)
223 223  )))
224 224  
225 225   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
226 226  
227 -
238 +\\
228 228  {{/layout-cell}}
229 229  {{/layout-section}}
230 230  
... ... @@ -232,28 +232,31 @@
232 232  {{layout-cell}}
233 233  **Check list:**
234 234  
235 -(% style="color:#ff0000" %)//always after entering the hutch!//
246 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
236 236  
237 -(% style="color:#000000" %)Click "Run" icon in kamzik.
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
238 238  
239 -* Put detector distance 200 in //prepare_for_measurement (      )//
240 -* Click "<Call>" next to //prepare_for_measurement//
241 -This will:
250 +* Put detector distance 200 in //prepare_for_measurement (      )
251 +//
252 +* Click "<Call>" next to //prepare_for_measurement
253 +//This will:\\
242 242  ** drive the collimator in //IN// position
243 243  ** drive detector to 200 mm
244 244  
257 +\\
245 245  
246 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
247 247  
261 +\\
248 248  
249 249  //**Set run parameters and go 🏃💥**//
250 250  
251 251  1. Set your desired No. of frames
252 -1. Enter the protein ID of your crystal sample
253 253  1. Match exposure time with chopper setting or set desired exposure time
254 254  1. Check trigger setting and match to chopper setting
255 -no chopper → external triffer //off//
256 - chopper → external trigger// on//
268 +no chopper → external triffer //off
269 +// chopper → external trigger// on
270 +//
257 257  1. To start the run, click "<Call>" next to //start_run (exposure    )//
258 258  {{/layout-cell}}
259 259  
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264 264  
265 265  {{layout-section ac:type="single"}}
266 266  {{layout-cell}}
267 -(% class="relative-table wrapped" style="width:55.9569%" %)
281 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
268 268  |=(((
269 269  Parameter
270 270  )))|=(((
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286 286  )))|(((
287 287  exposure time of Eiger
288 288  
289 -
303 +\\
290 290  )))|(% colspan="1" %)(((
291 -with chopper         → opening time displayed in chopper GUI
305 +chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
306 +
307 +chopper at 66 Hz   → 7.7 ms
308 +
292 292  no chopper            → 7.7 ms
293 293  
294 294  ----
... ... @@ -298,7 +298,7 @@
298 298  )))|(((
299 299  changes automatically
300 300  )))|(% colspan="1" %)(((
301 -
318 +\\
302 302  )))
303 303  |(% colspan="1" %)(((
304 304  Detector distance
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305 305  )))|(% colspan="1" %)(((
306 306  current detector postion readout
307 307  )))|(% colspan="1" %)(((
308 -
325 +\\
309 309  )))
310 -|(% colspan="1" %)(((
311 -protein ID
312 -)))|(% colspan="1" %)(((
313 -protein ID of crystal sample (see AMARCORD)
314 -)))|(% colspan="1" %)(((
315 -
316 -)))
317 317  
318 318  ----
319 319  {{/layout-cell}}
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333 333  {{/layout-cell}}
334 334  
335 335  {{layout-cell}}
336 -
346 +\\
337 337  
348 +\\
338 338  
350 +\\
339 339  
352 +\\
340 340  
354 +\\
341 341  
342 342  [[image:attach:safety_kamzik.PNG]]
343 343  {{/layout-cell}}
... ... @@ -356,6 +356,7 @@
356 356  * motor connected (icon green)?
357 357  )))
358 358  
373 +\\
359 359  
360 360  * (((
361 361  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
... ... @@ -365,6 +365,7 @@
365 365  * motor limits reached? → position displayed in red
366 366  )))
367 367  
383 +\\
368 368  
369 369  * (((
370 370  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
... ... @@ -374,6 +374,7 @@
374 374  * Nozzle or lines clogged? → flush with water, change nozzle
375 375  )))
376 376  
393 +\\
377 377  
378 378  * (((
379 379  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
... ... @@ -381,15 +381,12 @@
381 381  * First, restart kamzik (server+client) and see if this solves the issue
382 382  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
383 383  * (((
384 -If nothing works, kill the Simplon process and then start the server again:*
385 -
386 -(((
401 +If nothing works, kill the Simplon process and then start the server again:* (((
387 387  (% class="code" %)
388 388  (((
389 389  ssh haspp11exp03
390 390  )))
391 391  )))
392 -
393 393  * (((
394 394  (% class="code" %)
395 395  (((
... ... @@ -403,7 +403,6 @@
403 403  )))
404 404  )))
405 405  )))
406 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
407 407  )))
408 408  {{/layout-cell}}
409 409  {{/layout-section}}
... ... @@ -410,7 +410,7 @@
410 410  
411 411  {{layout-section ac:type="single"}}
412 412  {{layout-cell}}
413 -
426 +\\
414 414  {{/layout-cell}}
415 415  {{/layout-section}}
416 416  {{/layout}}
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1 -https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/281980768/14. Serial Crystallography: CFEL TapeDrive