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Last modified by chatzies on 2025-11-27 11:35
From version 50.1
edited by ahenkel
on 2022-04-04 19:18
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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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1 1  {{layout}}
2 2  {{layout-section ac:type="single"}}
3 3  {{layout-cell}}
4 -[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
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}}
... ... @@ -204,17 +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//
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  
... ... @@ -228,64 +228,53 @@
228 228  
229 229  (% class="code" %)
230 230  (((
231 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
221 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
232 232   password: written on control laptop (changes every 6 months)
233 233  )))
234 234  
235 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
225 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
236 236  
237 -\\
238 -
239 -Click "Start" icon in kamzik.
240 -
241 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
242 -
243 -----
227 +
244 244  {{/layout-cell}}
245 245  {{/layout-section}}
246 246  
247 -{{layout-section ac:type="two_equal"}}
231 +{{layout-section ac:type="two_left_sidebar"}}
248 248  {{layout-cell}}
249 249  **Check list:**
250 250  
251 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
235 +(% style="color:#ff0000" %)//always after entering the hutch!//
252 252  
253 -* Open BS1  (//CrystalControl)//
254 -* Put collimator in (//CrystalControl)//
255 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
256 -* Open fast shutter (//CrystalControl)//
257 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
258 -* Close fast shutter (//CrystalControl)//
237 +(% style="color:#000000" %)Click "Run" icon in kamzik.
259 259  
260 -\\
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
261 261  
262 -**Set run parameters and go 🏃💥**
263 263  
264 -1. Set your desired No. of frames
265 -1. Match exposure time with chopper setting
266 -1. Check trigger setting and match to chopper setting
267 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
268 -1. To start the run, click "<Call>" next to //exposure time//
246 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
269 269  
270 -\\
271 271  
272 -(% style="color: rgb(153,51,102);" %)**//Current bug~://**
249 +//**Set run parameters and go 🏃💥**//
273 273  
274 -(% style="color: rgb(0,0,0);" %)You need to "Stop" run in kamzik manually after all images have been acquired. This moves the shield up and closes the fast shutter. Afterwards you can start a new run by clicking "<Call>".
251 +1. Set your desired No. of frames
252 +1. Enter the protein ID of your crystal sample
253 +1. Match exposure time with chopper setting or set desired exposure time
254 +1. Check trigger setting and match to chopper setting
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}}
275 275  
276 -
277 -(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
278 -
279 -(% class="code" %)
280 -(((
281 - cd /gpfs/current/raw/scan_frames
282 - watch "ls -lrt <run number>/ | tail"
283 -\\\\\\\\
284 -)))
260 +{{layout-cell}}
261 +[[image:attach:Kamzik_run(2).PNG]]
285 285  {{/layout-cell}}
263 +{{/layout-section}}
286 286  
265 +{{layout-section ac:type="single"}}
287 287  {{layout-cell}}
288 -(% class="wrapped relative-table" style="width: 100.0%;" %)
267 +(% class="relative-table wrapped" style="width:55.9569%" %)
289 289  |=(((
290 290  Parameter
291 291  )))|=(((
... ... @@ -296,7 +296,7 @@
296 296  |(((
297 297  Images number
298 298  )))|(((
299 -Set number of frames you want to collect
278 +number of frames you want to collect
300 300  )))|(% colspan="1" %)(((
301 301  usually 100k - 200k, but adjust according to hitrate
302 302  
... ... @@ -307,12 +307,9 @@
307 307  )))|(((
308 308  exposure time of Eiger
309 309  
310 -\\
289 +
311 311  )))|(% colspan="1" %)(((
312 -chopper at 133 Hz → 3.7 ms
313 -
314 -chopper at 66 Hz   → 7.7 ms
315 -
291 +with chopper         → opening time displayed in chopper GUI
316 316  no chopper            → 7.7 ms
317 317  
318 318  ----
... ... @@ -322,7 +322,7 @@
322 322  )))|(((
323 323  changes automatically
324 324  )))|(% colspan="1" %)(((
325 -\\
301 +
326 326  )))
327 327  |(% colspan="1" %)(((
328 328  Detector distance
... ... @@ -329,27 +329,44 @@
329 329  )))|(% colspan="1" %)(((
330 330  current detector postion readout
331 331  )))|(% colspan="1" %)(((
332 -\\
308 +
333 333  )))
334 334  |(% colspan="1" %)(((
335 -move_detector (distance)
311 +protein ID
336 336  )))|(% colspan="1" %)(((
337 -Set detector distance
313 +protein ID of crystal sample (see AMARCORD)
338 338  )))|(% colspan="1" %)(((
339 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
315 +
340 340  )))
341 -|(% colspan="1" %)(((
342 -Diode voltage
343 -)))|(% colspan="1" %)(((
344 -read out of diode
345 -)))|(% colspan="1" %)(((
346 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 
347 -Call local contact
348 -**
349 -)))
317 +
318 +----
350 350  {{/layout-cell}}
351 351  {{/layout-section}}
352 352  
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 +
353 353  {{layout-section ac:type="single"}}
354 354  {{layout-cell}}
355 355  ----
... ... @@ -363,7 +363,6 @@
363 363  * motor connected (icon green)?
364 364  )))
365 365  
366 -\\
367 367  
368 368  * (((
369 369  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
... ... @@ -373,7 +373,6 @@
373 373  * motor limits reached? → position displayed in red
374 374  )))
375 375  
376 -\\
377 377  
378 378  * (((
379 379  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
... ... @@ -382,16 +382,44 @@
382 382  * Sample empty?
383 383  * Nozzle or lines clogged? → flush with water, change nozzle
384 384  )))
376 +
377 +
385 385  * (((
386 386  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
387 387  
388 388  * First, restart kamzik (server+client) and see if this solves the issue
389 389  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
390 -* If nothing works, kill the Simplon process and then start the server again:
391 -** ssh haspp11exp03
392 -** ps -ef | grep Simplon
393 -** kill -9 simplon_process_id
383 +* (((
384 +If nothing works, kill the Simplon process and then start the server again:*
385 +
386 +(((
387 +(% class="code" %)
388 +(((
389 +ssh haspp11exp03
394 394  )))
391 +)))
392 +
393 +* (((
394 +(% class="code" %)
395 +(((
396 +ps -ef | grep Simplon
397 +)))
398 +)))
399 +* (((
400 +(% class="code" %)
401 +(((
402 +kill -9 simplon_process_id
403 +)))
404 +)))
405 +)))
406 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
407 +)))
395 395  {{/layout-cell}}
396 396  {{/layout-section}}
410 +
411 +{{layout-section ac:type="single"}}
412 +{{layout-cell}}
413 +
414 +{{/layout-cell}}
415 +{{/layout-section}}
397 397  {{/layout}}
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1 +235031805
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1 -https://confluence.desy.de/spaces/11/pages/250178622/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive