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Last modified by chatzies on 2025-11-27 11:35
From version 46.1
edited by ahenkel
on 2021-12-12 23:53
Change comment: There is no comment for this version
To version 78.1
edited by tabermah
on 2024-12-03 11:34
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 +08. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.ahenkel
1 +XWiki.tabermah
Content
... ... @@ -1,27 +1,30 @@
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  
10 +----
11 +
12 12  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
13 13  
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.
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.
15 15  
16 16  Preparation:
17 17  
18 -* 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
19 19  
20 20  [[image:attach:20211201_095534.jpg||height="250"]]
21 21  
22 -\\
23 23  
24 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
23 +----
24 +
25 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26 +
27 +*
25 25  ** ==
26 26  
27 27  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!**
... ... @@ -38,12 +38,15 @@
38 38  
39 39  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40 40  
41 -\\
42 42  
43 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
45 +----
46 +
47 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48 +
49 +*
44 44  ** ==
45 45  
46 -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.
47 47  Now start the client. Same thing, a terminal will open, shortly after a small window.
48 48  
49 49  Click 'Devices' in the **client session** to open the control window.
... ... @@ -51,31 +51,31 @@
51 51  
52 52  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
53 53  
54 -* Click on the 'main tape' icon
60 +* Click the 'main tape' icon
55 55  * Change the velocity by typing anything from **0.3-3.0 mm/s**
56 56  * Common velocity is 1.0-1.5 mm/s
57 57  * 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.
58 -\\
64 +
59 59  * [[image:attach:kamzik_tape.PNG||height="400"]]
60 60  
61 61  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
62 62  
63 -* Click an the 'nozzle' icon.
69 +* Click on the 'nozzle' icon.
64 64  * (((
65 65  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.
66 66  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
67 67  
68 68  
69 -(% 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" %)** !!!**(%%)
70 70  \\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.
71 71  
72 72  (% class="wrapped" %)
73 73  |=(((
74 -\\
80 +
75 75  )))|=(((
76 76  direction
77 77  )))|=(((
78 -recommended step size
84 +recommended step size
79 79  for visual adjustment
80 80  )))|=(% colspan="1" %)(((
81 81  recommended step size
... ... @@ -110,8 +110,7 @@
110 110  be careful with -z, tape could be pushed out of focus
111 111  )))
112 112  
113 -**
114 -\\**
119 +
115 115  )))
116 116  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
117 117  
... ... @@ -119,28 +119,23 @@
119 119  
120 120  * The chiller circulates fluid through the gas nozzle.
121 121  
122 -\\
123 -
124 124  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
125 125  
126 -\\
127 127  
128 128  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
129 129  
130 -\\
131 131  
132 132  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
133 133  
134 134   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
135 - password: //written on control laptop (changes every 6 months)
136 -//
136 + password: //written on control laptop (changes every 6 months)//
137 137  
138 -\\
139 139  
140 -\\
141 141  
142 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ==
140 +----
143 143  
142 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
143 +
144 144  The tape stops automatically at 98% used length, if you need to change the rolls for orther reasons, stop the tape (velocity = 0.0 mm/s).
145 145  
146 146  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -148,7 +148,7 @@
148 148  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
149 149  * Cut the first cm of the new tape roll, directly behind the black sticky part.
150 150  * 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.
151 -* Open magnetic tape stabilizer on the **left side**. //!!!BEAMSTOP!!!//
151 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
152 152  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
153 153  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
154 154  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -155,32 +155,31 @@
155 155  * Close tape stabilizer.
156 156  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
157 157  
158 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
159 -**
158 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
160 160  
161 -\\
162 162  
163 -\\
164 164  
165 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
166 -** ===
162 +
167 167  {{/layout-cell}}
168 168  {{/layout-section}}
169 169  
170 170  {{layout-section ac:type="single"}}
171 171  {{layout-cell}}
172 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ==
168 +----
173 173  
170 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
171 +
174 174  start chopper gui from terminal:
175 175  
176 176  (% class="code" %)
177 177  (((
178 - cd /gpfs/local/shared/ChopperControl
176 + cd /gpfs/local/shared/ChopperControl          
179 179  )))
180 180  
181 181  (% class="code" %)
182 182  (((
183 183   python chopperControl.py
182 +\\
184 184  )))
185 185  {{/layout-cell}}
186 186  {{/layout-section}}
... ... @@ -193,86 +193,75 @@
193 193  {{layout-cell}}
194 194  **Chopper → no Chopper**
195 195  
196 -* decrease frequency by max. 10 Hz steps\\
195 +* decrease frequency by max. 10 Hz steps
197 197  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
198 198  * at frequency = 10 Hz, click "Stop"
199 -* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
198 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
200 200  
201 -(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
200 +(% style="color:#000000" %)**no Chopper → Chopper**
202 202  
203 -* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
204 -* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
205 -** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
206 -* (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
202 +* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
203 +* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
204 +** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
205 +* (% 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//
207 207  {{/layout-cell}}
208 208  {{/layout-section}}
209 209  
210 210  {{layout-section ac:type="single"}}
211 211  {{layout-cell}}
212 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ==
211 +----
213 213  
213 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
214 +
214 214  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
215 215  
216 216  (% class="code" %)
217 217  (((
218 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
219 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
219 219   password: written on control laptop (changes every 6 months)
220 220  )))
221 221  
222 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
223 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
223 223  
224 -\\
225 -
226 -Click "Start" icon in kamzik.
227 -
228 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
229 -
230 -----
225 +
231 231  {{/layout-cell}}
232 232  {{/layout-section}}
233 233  
234 -{{layout-section ac:type="two_equal"}}
229 +{{layout-section ac:type="two_left_sidebar"}}
235 235  {{layout-cell}}
236 236  **Check list:**
237 237  
238 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
233 +(% style="color:#ff0000" %)//always after entering the hutch!//
239 239  
240 -* Open BS1  (//CrystalControl)//
241 -* Put collimator in (//CrystalControl)//
242 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
243 -* Open fast shutter (//CrystalControl)//
244 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
245 -* Close fast shutter (//CrystalControl)//
235 +(% style="color:#000000" %)Click "Run" icon in kamzik.
246 246  
247 -\\
237 +* Put detector distance 200 in //prepare_for_measurement (      )//
238 +* Click "<Call>" next to //prepare_for_measurement//
239 +This will:
240 +** drive the collimator in //IN// position
241 +** drive detector to 200 mm
248 248  
249 -**Set run parameters and go 🏃💥**
243 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
250 250  
245 +//**Set run parameters and go 🏃💥**//
246 +
251 251  1. Set your desired No. of frames
252 -1. Match exposure time with chopper setting
248 +1. Enter the protein ID of your crystal sample
249 +1. Match exposure time with chopper setting or set desired exposure time
253 253  1. Check trigger setting and match to chopper setting
254 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
255 -1. To start the run, click "<Call>" next to //exposure time//
251 +no chopper → external triffer //off//
252 + chopper → external trigger// on//
253 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
254 +{{/layout-cell}}
256 256  
257 -\\
258 -
259 -(% style="color: rgb(153,51,102);" %)**//Current bug~://**
260 -
261 -(% 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>".
262 -
263 -
264 -(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
265 -
266 -(% class="code" %)
267 -(((
268 - cd /gpfs/current/raw/scan_frames
269 - watch "ls -lrt <run number>/ | tail"
270 -\\\\\\\\
271 -)))
256 +{{layout-cell}}
257 +[[image:attach:Kamzik_run(2).PNG]]
272 272  {{/layout-cell}}
259 +{{/layout-section}}
273 273  
261 +{{layout-section ac:type="single"}}
274 274  {{layout-cell}}
275 -(% class="wrapped relative-table" style="width: 100.0%;" %)
263 +(% class="relative-table wrapped" style="width:55.9569%" %)
276 276  |=(((
277 277  Parameter
278 278  )))|=(((
... ... @@ -283,7 +283,7 @@
283 283  |(((
284 284  Images number
285 285  )))|(((
286 -Set number of frames you want to collect
274 +number of frames you want to collect
287 287  )))|(% colspan="1" %)(((
288 288  usually 100k - 200k, but adjust according to hitrate
289 289  
... ... @@ -294,12 +294,9 @@
294 294  )))|(((
295 295  exposure time of Eiger
296 296  
297 -\\
285 +
298 298  )))|(% colspan="1" %)(((
299 -chopper at 133 Hz → 3.7 ms
300 -
301 -chopper at 66 Hz   → 7.7 ms
302 -
287 +with chopper         → opening time displayed in chopper GUI
303 303  no chopper            → 7.7 ms
304 304  
305 305  ----
... ... @@ -309,7 +309,7 @@
309 309  )))|(((
310 310  changes automatically
311 311  )))|(% colspan="1" %)(((
312 -\\
297 +
313 313  )))
314 314  |(% colspan="1" %)(((
315 315  Detector distance
... ... @@ -316,32 +316,49 @@
316 316  )))|(% colspan="1" %)(((
317 317  current detector postion readout
318 318  )))|(% colspan="1" %)(((
319 -\\
304 +
320 320  )))
321 321  |(% colspan="1" %)(((
322 -move_detector (distance)
307 +protein ID
323 323  )))|(% colspan="1" %)(((
324 -Set detector distance
309 +protein ID of crystal sample (see AMARCORD)
325 325  )))|(% colspan="1" %)(((
326 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
311 +
327 327  )))
328 -|(% colspan="1" %)(((
329 -Diode voltage
330 -)))|(% colspan="1" %)(((
331 -read out of diode
332 -)))|(% colspan="1" %)(((
333 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 
334 -Call local contact
335 -**
336 -)))
313 +
314 +----
337 337  {{/layout-cell}}
338 338  {{/layout-section}}
339 339  
318 +{{layout-section ac:type="two_equal"}}
319 +{{layout-cell}}
320 +**After data collection/Before entering the exp. hutch:**
321 +
322 +1. Go to "Safety" in kamzik.
323 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
324 +11. Drive the collimator out
325 +11. Drive the detector back to 1500 mm
326 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
327 +
328 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
329 +{{/layout-cell}}
330 +
331 +{{layout-cell}}
332 +
333 +
334 +
335 +
336 +
337 +
338 +[[image:attach:safety_kamzik.PNG]]
339 +{{/layout-cell}}
340 +{{/layout-section}}
341 +
340 340  {{layout-section ac:type="single"}}
341 341  {{layout-cell}}
342 342  ----
343 343  
344 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}**14.9 Troubleshooting** ==
346 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
345 345  
346 346  * (((
347 347  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -350,8 +350,6 @@
350 350  * motor connected (icon green)?
351 351  )))
352 352  
353 -\\
354 -
355 355  * (((
356 356  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
357 357  
... ... @@ -360,8 +360,6 @@
360 360  * motor limits reached? → position displayed in red
361 361  )))
362 362  
363 -\\
364 -
365 365  * (((
366 366  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
367 367  
... ... @@ -369,6 +369,43 @@
369 369  * Sample empty?
370 370  * Nozzle or lines clogged? → flush with water, change nozzle
371 371  )))
370 +
371 +* (((
372 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
373 +
374 +* First, restart kamzik (server+client) and see if this solves the issue
375 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
376 +* (((
377 +If nothing works, kill the Simplon process and then start the server again:*
378 +
379 +(((
380 +(% class="code" %)
381 +(((
382 +ssh haspp11exp03
383 +)))
384 +)))
385 +
386 +* (((
387 +(% class="code" %)
388 +(((
389 +ps -ef | grep Simplon
390 +)))
391 +)))
392 +* (((
393 +(% class="code" %)
394 +(((
395 +kill -9 simplon_process_id
396 +)))
397 +)))
398 +)))
399 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
400 +)))
372 372  {{/layout-cell}}
373 373  {{/layout-section}}
403 +
404 +{{layout-section ac:type="single"}}
405 +{{layout-cell}}
406 +
407 +{{/layout-cell}}
408 +{{/layout-section}}
374 374  {{/layout}}
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