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

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Title
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1 -14. Serial Crystallography: CFEL TapeDrive
1 +10. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.ahenkel
1 +XWiki.tabermah
Content
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3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 -\\
7 7  
8 8  {{toc minLevel="2"/}}
9 9  
10 -\\
11 11  
12 12  ----
13 13  
... ... @@ -21,11 +21,12 @@
21 21  
22 22  [[image:attach:20211201_095534.jpg||height="250"]]
23 23  
24 -\\
25 25  
26 26  ----
27 27  
28 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
25 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26 +
27 +*
29 29  ** ==
30 30  
31 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!**
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42 42  
43 43  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
44 44  
45 -\\
46 46  
47 47  ----
48 48  
49 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
47 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48 +
49 +*
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.
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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: 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);" %)** !!!**(%%)
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" %)** !!!**(%%)
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
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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  
... ... @@ -125,25 +125,19 @@
125 125  
126 126  * The chiller circulates fluid through the gas nozzle.
127 127  
128 -\\
129 129  
130 130  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
131 131  
132 -\\
133 133  
134 134  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
135 135  
136 -\\
137 137  
138 138  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
139 139  
140 140   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
141 - password: //written on control laptop (changes every 6 months)
142 -//
138 + password: //written on control laptop (changes every 6 months)//
143 143  
144 -\\
145 145  
146 -\\
147 147  
148 148  ----
149 149  
... ... @@ -156,7 +156,7 @@
156 156  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
157 157  * Cut the first cm of the new tape roll, directly behind the black sticky part.
158 158  * 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.
159 -* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
153 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
160 160  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
161 161  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
162 162  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -163,15 +163,11 @@
163 163  * Close tape stabilizer.
164 164  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
165 165  
166 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 -**
160 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
168 168  
169 -\\
170 170  
171 -\\
172 172  
173 -**
174 -**
164 +
175 175  {{/layout-cell}}
176 176  {{/layout-section}}
177 177  
... ... @@ -185,13 +185,13 @@
185 185  
186 186  (% class="code" %)
187 187  (((
188 - cd /gpfs/local/shared/ChopperControl
178 + cd /gpfs/local/shared/ChopperControl          
189 189  )))
190 190  
191 191  (% class="code" %)
192 192  (((
193 193   python chopperControl.py
194 -\\\\
184 +\\
195 195  )))
196 196  {{/layout-cell}}
197 197  {{/layout-section}}
... ... @@ -204,18 +204,17 @@
204 204  {{layout-cell}}
205 205  **Chopper → no Chopper**
206 206  
207 -* decrease frequency by max. 10 Hz steps\\
197 +* decrease frequency by max. 10 Hz steps
208 208  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
209 209  * at frequency = 10 Hz, click "Stop"
210 -* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
200 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
211 211  
212 -(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
202 +(% style="color:#000000" %)**no Chopper → Chopper**
213 213  
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 -//
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//
219 219  {{/layout-cell}}
220 220  {{/layout-section}}
221 221  
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229 229  
230 230  (% class="code" %)
231 231  (((
232 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
221 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
233 233   password: written on control laptop (changes every 6 months)
234 234  )))
235 235  
236 236   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
237 237  
238 -\\
227 +
239 239  {{/layout-cell}}
240 240  {{/layout-section}}
241 241  
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243 243  {{layout-cell}}
244 244  **Check list:**
245 245  
246 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
235 +(% style="color:#ff0000" %)//always after entering the hutch!//
247 247  
248 -(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
237 +(% style="color:#000000" %)Click "Run" icon in kamzik.
249 249  
250 -* Put detector distance 200 in //prepare_for_measurement (      )
251 -//
252 -* Click "<Call>" next to //prepare_for_measurement
253 -//This will:\\
239 +* Put detector distance 200 in //prepare_for_measurement (      )//
240 +* Click "<Call>" next to //prepare_for_measurement//
241 +This will:
254 254  ** drive the collimator in //IN// position
255 255  ** drive detector to 200 mm
256 256  
257 -\\
258 258  
259 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
246 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
260 260  
261 -\\
262 262  
263 263  //**Set run parameters and go 🏃💥**//
264 264  
265 265  1. Set your desired No. of frames
252 +1. Enter the protein ID of your crystal sample
266 266  1. Match exposure time with chopper setting or set desired exposure time
267 267  1. Check trigger setting and match to chopper setting
268 -no chopper → external triffer //off
269 -// chopper → external trigger// on
270 -//
255 +no chopper → external triffer //off//
256 + chopper → external trigger// on//
271 271  1. To start the run, click "<Call>" next to //start_run (exposure    )//
272 272  {{/layout-cell}}
273 273  
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278 278  
279 279  {{layout-section ac:type="single"}}
280 280  {{layout-cell}}
281 -(% class="relative-table wrapped" style="width: 55.9569%;" %)
267 +(% class="relative-table wrapped" style="width:55.9569%" %)
282 282  |=(((
283 283  Parameter
284 284  )))|=(((
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300 300  )))|(((
301 301  exposure time of Eiger
302 302  
303 -\\
289 +
304 304  )))|(% colspan="1" %)(((
305 -chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
306 -
307 -chopper at 66 Hz   → 7.7 ms
308 -
291 +with chopper         → opening time displayed in chopper GUI
309 309  no chopper            → 7.7 ms
310 310  
311 311  ----
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315 315  )))|(((
316 316  changes automatically
317 317  )))|(% colspan="1" %)(((
318 -\\
301 +
319 319  )))
320 320  |(% colspan="1" %)(((
321 321  Detector distance
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322 322  )))|(% colspan="1" %)(((
323 323  current detector postion readout
324 324  )))|(% colspan="1" %)(((
325 -\\
308 +
326 326  )))
310 +|(% colspan="1" %)(((
311 +protein ID
312 +)))|(% colspan="1" %)(((
313 +protein ID of crystal sample (see AMARCORD)
314 +)))|(% colspan="1" %)(((
315 +
316 +)))
327 327  
328 328  ----
329 329  {{/layout-cell}}
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343 343  {{/layout-cell}}
344 344  
345 345  {{layout-cell}}
346 -\\
336 +
347 347  
348 -\\
349 349  
350 -\\
351 351  
352 -\\
353 353  
354 -\\
355 355  
356 356  [[image:attach:safety_kamzik.PNG]]
357 357  {{/layout-cell}}
... ... @@ -370,7 +370,6 @@
370 370  * motor connected (icon green)?
371 371  )))
372 372  
373 -\\
374 374  
375 375  * (((
376 376  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
... ... @@ -380,7 +380,6 @@
380 380  * motor limits reached? → position displayed in red
381 381  )))
382 382  
383 -\\
384 384  
385 385  * (((
386 386  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
... ... @@ -390,7 +390,6 @@
390 390  * Nozzle or lines clogged? → flush with water, change nozzle
391 391  )))
392 392  
393 -\\
394 394  
395 395  * (((
396 396  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
... ... @@ -398,12 +398,15 @@
398 398  * First, restart kamzik (server+client) and see if this solves the issue
399 399  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
400 400  * (((
401 -If nothing works, kill the Simplon process and then start the server again:* (((
384 +If nothing works, kill the Simplon process and then start the server again:*
385 +
386 +(((
402 402  (% class="code" %)
403 403  (((
404 404  ssh haspp11exp03
405 405  )))
406 406  )))
392 +
407 407  * (((
408 408  (% class="code" %)
409 409  (((
... ... @@ -417,6 +417,7 @@
417 417  )))
418 418  )))
419 419  )))
406 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
420 420  )))
421 421  {{/layout-cell}}
422 422  {{/layout-section}}
... ... @@ -423,7 +423,7 @@
423 423  
424 424  {{layout-section ac:type="single"}}
425 425  {{layout-cell}}
426 -\\
413 +
427 427  {{/layout-cell}}
428 428  {{/layout-section}}
429 429  {{/layout}}
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1 +235031805
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1 -https://confluence.desy.de/spaces/11/pages/281980768/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive