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Last modified by chatzies on 2025-11-27 11:35
From version 67.1
edited by ahenkel
on 2022-05-07 18:33
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
... ... @@ -3,11 +3,9 @@
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!**
... ... @@ -42,14 +42,15 @@
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.
... ... @@ -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: 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
... ... @@ -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  
... ... @@ -125,25 +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}}
... ... @@ -204,23 +204,24 @@
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  
222 222  {{layout-section ac:type="single"}}
223 223  {{layout-cell}}
213 +----
214 +
224 224  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
225 225  
226 226  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
... ... @@ -227,13 +227,13 @@
227 227  
228 228  (% class="code" %)
229 229  (((
230 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
221 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
231 231   password: written on control laptop (changes every 6 months)
232 232  )))
233 233  
234 234   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
235 235  
236 -\\
227 +
237 237  {{/layout-cell}}
238 238  {{/layout-section}}
239 239  
... ... @@ -241,62 +241,39 @@
241 241  {{layout-cell}}
242 242  **Check list:**
243 243  
244 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
235 +(% style="color:#ff0000" %)//always after entering the hutch!//
245 245  
246 -(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
237 +(% style="color:#000000" %)Click "Run" icon in kamzik.
247 247  
248 -* Put collimator in
249 -** Put detector distance 200 in //prepare_for_measurement (      )
250 -//
251 -** Click "<Call>" next to //prepare_for_measurement//
239 +* Put detector distance 200 in //prepare_for_measurement (      )//
240 +* Click "<Call>" next to //prepare_for_measurement//
241 +This will:
242 +** drive the collimator in //IN// position
243 +** drive detector to 200 mm
252 252  
253 -\\
254 254  
255 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
256 -{{/layout-cell}}
246 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
257 257  
258 -{{layout-cell}}
259 -[[image:attach:kamzik_safety.PNG||height="400"]]
260 -{{/layout-cell}}
261 -{{/layout-section}}
262 262  
263 -{{layout-section ac:type="single"}}
264 -{{layout-cell}}
265 -----
249 +//**Set run parameters and go 🏃💥**//
266 266  
267 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
268 -
269 -----
270 -{{/layout-cell}}
271 -{{/layout-section}}
272 -
273 -{{layout-section ac:type="two_equal"}}
274 -{{layout-cell}}
275 -**Set run parameters and go 🏃💥**
276 -
277 277  1. Set your desired No. of frames
252 +1. Enter the protein ID of your crystal sample
278 278  1. Match exposure time with chopper setting or set desired exposure time
279 279  1. Check trigger setting and match to chopper setting
280 -1. To start the run, click "<Call>" next to //start_run (exposure    )
281 -//
255 +no chopper → external triffer //off//
256 + chopper → external trigger// on//
257 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
258 +{{/layout-cell}}
282 282  
283 -\\
284 -
285 -\\
286 -
287 -**After data collection/Before entering the exp. hutch:**
288 -
289 -1. Go to "Safety" in kamzik.
290 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
291 -11. Drive the collimator out
292 -11. Drive the detector back to 1500 mm
293 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
294 -
295 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
260 +{{layout-cell}}
261 +[[image:attach:Kamzik_run(2).PNG]]
296 296  {{/layout-cell}}
263 +{{/layout-section}}
297 297  
265 +{{layout-section ac:type="single"}}
298 298  {{layout-cell}}
299 -(% class="wrapped relative-table" style="width: 100.0%;" %)
267 +(% class="relative-table wrapped" style="width:55.9569%" %)
300 300  |=(((
301 301  Parameter
302 302  )))|=(((
... ... @@ -307,7 +307,7 @@
307 307  |(((
308 308  Images number
309 309  )))|(((
310 -Set number of frames you want to collect
278 +number of frames you want to collect
311 311  )))|(% colspan="1" %)(((
312 312  usually 100k - 200k, but adjust according to hitrate
313 313  
... ... @@ -318,12 +318,9 @@
318 318  )))|(((
319 319  exposure time of Eiger
320 320  
321 -\\
289 +
322 322  )))|(% colspan="1" %)(((
323 -chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
324 -
325 -chopper at 66 Hz   → 7.7 ms
326 -
291 +with chopper         → opening time displayed in chopper GUI
327 327  no chopper            → 7.7 ms
328 328  
329 329  ----
... ... @@ -333,7 +333,7 @@
333 333  )))|(((
334 334  changes automatically
335 335  )))|(% colspan="1" %)(((
336 -\\
301 +
337 337  )))
338 338  |(% colspan="1" %)(((
339 339  Detector distance
... ... @@ -340,18 +340,44 @@
340 340  )))|(% colspan="1" %)(((
341 341  current detector postion readout
342 342  )))|(% colspan="1" %)(((
343 -\\
308 +
344 344  )))
345 345  |(% colspan="1" %)(((
346 -move_detector (distance)
311 +protein ID
347 347  )))|(% colspan="1" %)(((
348 -Set detector distance
313 +protein ID of crystal sample (see AMARCORD)
349 349  )))|(% colspan="1" %)(((
350 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
315 +
351 351  )))
317 +
318 +----
352 352  {{/layout-cell}}
353 353  {{/layout-section}}
354 354  
322 +{{layout-section ac:type="two_equal"}}
323 +{{layout-cell}}
324 +**After data collection/Before entering the exp. hutch:**
325 +
326 +1. Go to "Safety" in kamzik.
327 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
328 +11. Drive the collimator out
329 +11. Drive the detector back to 1500 mm
330 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
331 +
332 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
333 +{{/layout-cell}}
334 +
335 +{{layout-cell}}
336 +
337 +
338 +
339 +
340 +
341 +
342 +[[image:attach:safety_kamzik.PNG]]
343 +{{/layout-cell}}
344 +{{/layout-section}}
345 +
355 355  {{layout-section ac:type="single"}}
356 356  {{layout-cell}}
357 357  ----
... ... @@ -365,7 +365,6 @@
365 365  * motor connected (icon green)?
366 366  )))
367 367  
368 -\\
369 369  
370 370  * (((
371 371  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
... ... @@ -375,7 +375,6 @@
375 375  * motor limits reached? → position displayed in red
376 376  )))
377 377  
378 -\\
379 379  
380 380  * (((
381 381  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
... ... @@ -385,7 +385,6 @@
385 385  * Nozzle or lines clogged? → flush with water, change nozzle
386 386  )))
387 387  
388 -\\
389 389  
390 390  * (((
391 391  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
... ... @@ -393,12 +393,15 @@
393 393  * First, restart kamzik (server+client) and see if this solves the issue
394 394  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
395 395  * (((
396 -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 +(((
397 397  (% class="code" %)
398 398  (((
399 399  ssh haspp11exp03
400 400  )))
401 401  )))
392 +
402 402  * (((
403 403  (% class="code" %)
404 404  (((
... ... @@ -412,6 +412,7 @@
412 412  )))
413 413  )))
414 414  )))
406 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
415 415  )))
416 416  {{/layout-cell}}
417 417  {{/layout-section}}
... ... @@ -418,7 +418,7 @@
418 418  
419 419  {{layout-section ac:type="single"}}
420 420  {{layout-cell}}
421 -\\
413 +
422 422  {{/layout-cell}}
423 423  {{/layout-section}}
424 424  {{/layout}}
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1 -254729368
1 +235031805
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1 -https://confluence.desy.de/spaces/11/pages/254729368/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive