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Last modified by chatzies on 2025-11-27 11:35
From version 54.1
edited by ahenkel
on 2022-04-04 19:58
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
... ... @@ -3,29 +3,28 @@
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  
14 14  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
15 15  
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.
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.
17 17  
18 18  Preparation:
19 19  
20 -* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
18 +* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
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.
... ... @@ -57,31 +57,31 @@
57 57  
58 58  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
59 59  
60 -* Click on the 'main tape' icon
60 +* Click the 'main tape' icon
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** ====
68 68  
69 -* Click an the 'nozzle' icon.
69 +* Click on the 'nozzle' icon.
70 70  * (((
71 71  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.
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**. //!!!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}}
... ... @@ -204,22 +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//
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//
218 218  {{/layout-cell}}
219 219  {{/layout-section}}
220 220  
221 -{{layout-section ac:type="two_equal"}}
211 +{{layout-section ac:type="single"}}
222 222  {{layout-cell}}
213 +----
214 +
223 223  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
224 224  
225 225  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
... ... @@ -226,72 +226,53 @@
226 226  
227 227  (% class="code" %)
228 228  (((
229 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
221 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
230 230   password: written on control laptop (changes every 6 months)
231 231  )))
232 232  
233 233   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
234 234  
235 -\\
227 +
228 +{{/layout-cell}}
229 +{{/layout-section}}
236 236  
231 +{{layout-section ac:type="two_left_sidebar"}}
232 +{{layout-cell}}
237 237  **Check list:**
238 238  
239 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
235 +(% style="color:#ff0000" %)//always after entering the hutch!//
240 240  
241 -(% style="color: rgb(0,0,0);" %)Click "Safety" icon in kamzik.
237 +(% style="color:#000000" %)Click "Run" icon in kamzik.
242 242  
243 -* Put collimator in
244 -** Click "<Call>" next to //collimator_in//
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
245 245  
246 -\\
247 247  
248 -* Open beam shutter BS1 in //CrystalControl//
249 -{{/layout-cell}}
246 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
250 250  
251 -{{layout-cell}}
252 -[[image:attach:kamzik_safety.PNG||height="400"]]
253 -{{/layout-cell}}
254 -{{/layout-section}}
255 255  
256 -{{layout-section ac:type="single"}}
257 -{{layout-cell}}
258 -----
249 +//**Set run parameters and go 🏃💥**//
259 259  
260 -Click "Start/Run" icon in kamzik.
261 -
262 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
263 -
264 -----
265 -{{/layout-cell}}
266 -{{/layout-section}}
267 -
268 -{{layout-section ac:type="two_equal"}}
269 -{{layout-cell}}
270 -**Set run parameters and go 🏃💥**
271 -
272 272  1. Set your desired No. of frames
273 -1. Match exposure time with chopper setting
252 +1. Enter the protein ID of your crystal sample
253 +1. Match exposure time with chopper setting or set desired exposure time
274 274  1. Check trigger setting and match to chopper setting
275 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
276 -1. To start the run, click "<Call>" next to //exposure time//
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}}
277 277  
278 -\\
279 -
280 -\\
281 -
282 -**After data collection/Before entering the exp. hutch:**
283 -
284 -1. Go to "Safety" in kamzik.
285 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
286 -11. Drive the collimator out
287 -11. Drive the detector back to 1500 mm
288 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
289 -
290 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
260 +{{layout-cell}}
261 +[[image:attach:Kamzik_run(2).PNG]]
291 291  {{/layout-cell}}
263 +{{/layout-section}}
292 292  
265 +{{layout-section ac:type="single"}}
293 293  {{layout-cell}}
294 -(% class="wrapped relative-table" style="width: 100.0%;" %)
267 +(% class="relative-table wrapped" style="width:55.9569%" %)
295 295  |=(((
296 296  Parameter
297 297  )))|=(((
... ... @@ -302,7 +302,7 @@
302 302  |(((
303 303  Images number
304 304  )))|(((
305 -Set number of frames you want to collect
278 +number of frames you want to collect
306 306  )))|(% colspan="1" %)(((
307 307  usually 100k - 200k, but adjust according to hitrate
308 308  
... ... @@ -313,12 +313,9 @@
313 313  )))|(((
314 314  exposure time of Eiger
315 315  
316 -\\
289 +
317 317  )))|(% colspan="1" %)(((
318 -chopper at 133 Hz → 3.7 ms
319 -
320 -chopper at 66 Hz   → 7.7 ms
321 -
291 +with chopper         → opening time displayed in chopper GUI
322 322  no chopper            → 7.7 ms
323 323  
324 324  ----
... ... @@ -328,7 +328,7 @@
328 328  )))|(((
329 329  changes automatically
330 330  )))|(% colspan="1" %)(((
331 -\\
301 +
332 332  )))
333 333  |(% colspan="1" %)(((
334 334  Detector distance
... ... @@ -335,27 +335,44 @@
335 335  )))|(% colspan="1" %)(((
336 336  current detector postion readout
337 337  )))|(% colspan="1" %)(((
338 -\\
308 +
339 339  )))
340 340  |(% colspan="1" %)(((
341 -move_detector (distance)
311 +protein ID
342 342  )))|(% colspan="1" %)(((
343 -Set detector distance
313 +protein ID of crystal sample (see AMARCORD)
344 344  )))|(% colspan="1" %)(((
345 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
315 +
346 346  )))
347 -|(% colspan="1" %)(((
348 -Diode voltage
349 -)))|(% colspan="1" %)(((
350 -read out of diode
351 -)))|(% colspan="1" %)(((
352 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 
353 -Call local contact
354 -**
355 -)))
317 +
318 +----
356 356  {{/layout-cell}}
357 357  {{/layout-section}}
358 358  
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 +
359 359  {{layout-section ac:type="single"}}
360 360  {{layout-cell}}
361 361  ----
... ... @@ -369,7 +369,6 @@
369 369  * motor connected (icon green)?
370 370  )))
371 371  
372 -\\
373 373  
374 374  * (((
375 375  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
... ... @@ -379,7 +379,6 @@
379 379  * motor limits reached? → position displayed in red
380 380  )))
381 381  
382 -\\
383 383  
384 384  * (((
385 385  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
... ... @@ -389,7 +389,6 @@
389 389  * Nozzle or lines clogged? → flush with water, change nozzle
390 390  )))
391 391  
392 -\\
393 393  
394 394  * (((
395 395  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
... ... @@ -397,12 +397,15 @@
397 397  * First, restart kamzik (server+client) and see if this solves the issue
398 398  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
399 399  * (((
400 -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 +(((
401 401  (% class="code" %)
402 402  (((
403 403  ssh haspp11exp03
404 404  )))
405 405  )))
392 +
406 406  * (((
407 407  (% class="code" %)
408 408  (((
... ... @@ -416,6 +416,7 @@
416 416  )))
417 417  )))
418 418  )))
406 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
419 419  )))
420 420  {{/layout-cell}}
421 421  {{/layout-section}}
... ... @@ -422,7 +422,7 @@
422 422  
423 423  {{layout-section ac:type="single"}}
424 424  {{layout-cell}}
425 -\\
413 +
426 426  {{/layout-cell}}
427 427  {{/layout-section}}
428 428  {{/layout}}
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1 -250178642
1 +235031805
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1 -https://confluence.desy.de/spaces/11/pages/250178642/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive