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Last modified by chatzies on 2025-11-27 11:35
From version 88.1
edited by chatzies
on 2025-11-27 11:35
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To version 67.1
edited by ahenkel
on 2022-05-07 18:33
Change comment: There is no comment for this version

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Title
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1 -CFEL TapeDrive: Serial Crystallography
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.chatzies
1 +XWiki.ahenkel
Content
... ... @@ -3,28 +3,32 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 -{{toc/}}
8 +{{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 11  
12 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. Sample characteristics and preparation =
14 +== {{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.
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.
15 15  
16 16  Preparation:
17 17  
18 -* filter through 30 µm (green) or 50 µm (yellow) cell filter into an Eppendorf or Falcon (original!) tube
20 +* 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  
24 +\\
22 22  
23 23  ----
24 24  
25 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}8.2. Connecting sample to ElveFlow, sample exchange =
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
26 26  
27 -After filtration, screw the ElveFlow connector to your Eppendorf or Falcon tube. Make sure that the yellow-ish tube goes all the way 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!**
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!**
28 28  
29 29  Be aware to which channel and nozzle line your sample is connected.
30 30  
... ... @@ -38,30 +38,30 @@
38 38  
39 39  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40 40  
45 +\\
41 41  
42 42  ----
43 43  
44 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. TapeDrive operation =
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 +** ==
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.
47 -
52 +The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
48 48  Now start the client. Same thing, a terminal will open, shortly after a small window.
49 49  
50 50  Click 'Devices' in the **client session** to open the control window.
51 51  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
52 52  
53 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}Tape ==
58 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
54 54  
55 55  * Click the 'main tape' icon
56 56  * Change the velocity by typing anything from **0.3-3.0 mm/s**
57 57  * Common velocity is 1.0-1.5 mm/s
58 58  * 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 +\\
65 +* [[image:attach:kamzik_tape.PNG||height="400"]]
59 59  
60 -[[image:attach:kamzik_tape.PNG||height="400"]]
67 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
61 61  
62 -
63 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
64 -
65 65  * Click on the 'nozzle' icon.
66 66  * (((
67 67  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.
... ... @@ -68,16 +68,16 @@
68 68  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
69 69  
70 70  
71 -(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving the nozzle, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
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);" %)** !!!**(%%)
72 72  \\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.
73 73  
74 74  (% class="wrapped" %)
75 75  |=(((
76 -
80 +\\
77 77  )))|=(((
78 78  direction
79 79  )))|=(((
80 -recommended step size
84 +recommended step size
81 81  for visual adjustment
82 82  )))|=(% colspan="1" %)(((
83 83  recommended step size
... ... @@ -112,32 +112,38 @@
112 112  be careful with -z, tape could be pushed out of focus
113 113  )))
114 114  
115 -
119 +**
120 +\\**
116 116  )))
122 +* [[image:attach:kamzik_nozzle.PNG||height="400"]]
117 117  
118 -[[image:attach:kamzik_nozzle.PNG||height="400"]]
124 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
119 119  
120 -
121 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
122 -
123 123  * The chiller circulates fluid through the gas nozzle.
124 124  
125 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
128 +\\
126 126  
130 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
127 127  
128 -== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
132 +\\
129 129  
134 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
130 130  
136 +\\
137 +
131 131  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
132 132  
133 133   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
134 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
135 135  
144 +\\
136 136  
146 +\\
137 137  
138 138  ----
139 139  
140 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
141 141  
142 142  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).
143 143  
... ... @@ -146,7 +146,7 @@
146 146  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
147 147  * Cut the first cm of the new tape roll, directly behind the black sticky part.
148 148  * 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.
149 -* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
150 150  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
151 151  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
152 152  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -153,9 +153,15 @@
153 153  * Close tape stabilizer.
154 154  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
155 155  
156 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
166 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 +**
157 157  
158 -
169 +\\
170 +
171 +\\
172 +
173 +**
174 +**
159 159  {{/layout-cell}}
160 160  {{/layout-section}}
161 161  
... ... @@ -163,18 +163,19 @@
163 163  {{layout-cell}}
164 164  ----
165 165  
166 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
167 167  
168 168  start chopper gui from terminal:
169 169  
170 170  (% class="code" %)
171 171  (((
172 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
173 173  )))
174 174  
175 175  (% class="code" %)
176 176  (((
177 177   python chopperControl.py
194 +\\\\
178 178  )))
179 179  {{/layout-cell}}
180 180  {{/layout-section}}
... ... @@ -187,37 +187,36 @@
187 187  {{layout-cell}}
188 188  **Chopper → no Chopper**
189 189  
190 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
191 191  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
192 192  * at frequency = 10 Hz, click "Stop"
193 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
194 194  
195 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
196 196  
197 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
198 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
199 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
200 -* (% 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//
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 +//
201 201  {{/layout-cell}}
202 202  {{/layout-section}}
203 203  
204 204  {{layout-section ac:type="single"}}
205 205  {{layout-cell}}
206 -----
224 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
207 207  
208 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
209 -
210 210  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
211 211  
212 212  (% class="code" %)
213 213  (((
214 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
230 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
215 215   password: written on control laptop (changes every 6 months)
216 216  )))
217 217  
218 218   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
219 219  
220 -
236 +\\
221 221  {{/layout-cell}}
222 222  {{/layout-section}}
223 223  
... ... @@ -225,37 +225,62 @@
225 225  {{layout-cell}}
226 226  **Check list:**
227 227  
228 -(% style="color:#ff0000" %)//always after entering the hutch!//
244 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
229 229  
230 -(% style="color:#000000" %)Click "Run" icon in kamzik.
246 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
231 231  
232 -* Put detector distance 200 mm in //prepare_for_measurement (      )//
233 -* Click "<Call>" next to //prepare_for_measurement//
234 -This will:
235 -** drive the collimator in //IN// position
236 -** drive detector to 200 mm
248 +* Put collimator in
249 +** Put detector distance 200 in //prepare_for_measurement (      )
250 +//
251 +** Click "<Call>" next to //prepare_for_measurement//
237 237  
238 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
253 +\\
239 239  
240 -//**Set run parameters and go 🏃💥**//
241 -
242 -1. Set your desired No. of frames
243 -1. Enter the protein ID of your crystal sample
244 -1. Match exposure time with chopper setting or set desired exposure time
245 -1. Check trigger setting and match to chopper setting
246 -no chopper → external triffer //off//
247 - chopper → external trigger// on//
248 -1. To start the run, click "<Call>" next to //start_run (exposure    )//
255 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
249 249  {{/layout-cell}}
250 250  
251 251  {{layout-cell}}
252 -[[image:attach:Kamzik_run(2).PNG]]
259 +[[image:attach:kamzik_safety.PNG||height="400"]]
253 253  {{/layout-cell}}
254 254  {{/layout-section}}
255 255  
256 256  {{layout-section ac:type="single"}}
257 257  {{layout-cell}}
258 -(% class="relative-table wrapped" style="width:55.9569%" %)
265 +----
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 +1. Set your desired No. of frames
278 +1. Match exposure time with chopper setting or set desired exposure time
279 +1. Check trigger setting and match to chopper setting
280 +1. To start the run, click "<Call>" next to //start_run (exposure    )
281 +//
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"]]
296 +{{/layout-cell}}
297 +
298 +{{layout-cell}}
299 +(% class="wrapped relative-table" style="width: 100.0%;" %)
259 259  |=(((
260 260  Parameter
261 261  )))|=(((
... ... @@ -266,7 +266,7 @@
266 266  |(((
267 267  Images number
268 268  )))|(((
269 -number of frames you want to collect
310 +Set number of frames you want to collect
270 270  )))|(% colspan="1" %)(((
271 271  usually 100k - 200k, but adjust according to hitrate
272 272  
... ... @@ -277,9 +277,12 @@
277 277  )))|(((
278 278  exposure time of Eiger
279 279  
280 -
321 +\\
281 281  )))|(% colspan="1" %)(((
282 -with chopper         → opening time displayed in chopper GUI
323 +chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
324 +
325 +chopper at 66 Hz   → 7.7 ms
326 +
283 283  no chopper            → 7.7 ms
284 284  
285 285  ----
... ... @@ -289,7 +289,7 @@
289 289  )))|(((
290 290  changes automatically
291 291  )))|(% colspan="1" %)(((
292 -
336 +\\
293 293  )))
294 294  |(% colspan="1" %)(((
295 295  Detector distance
... ... @@ -296,55 +296,35 @@
296 296  )))|(% colspan="1" %)(((
297 297  current detector postion readout
298 298  )))|(% colspan="1" %)(((
299 -
343 +\\
300 300  )))
301 301  |(% colspan="1" %)(((
302 -protein ID
346 +move_detector (distance)
303 303  )))|(% colspan="1" %)(((
304 -protein ID of crystal sample (see AMARCORD)
348 +Set detector distance
305 305  )))|(% colspan="1" %)(((
306 -
350 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
307 307  )))
308 -
309 -----
310 310  {{/layout-cell}}
311 311  {{/layout-section}}
312 312  
313 -{{layout-section ac:type="two_equal"}}
314 -{{layout-cell}}
315 -**After data collection/Before entering the exp. hutch:**
316 -
317 -1. Go to "Safety" in kamzik.
318 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
319 -11. Drive the collimator out
320 -11. Drive the detector back to 1500 mm
321 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
322 -
323 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
324 -{{/layout-cell}}
325 -
326 -{{layout-cell}}
327 -
328 -
329 -[[image:attach:safety_kamzik.PNG]]
330 -{{/layout-cell}}
331 -{{/layout-section}}
332 -
333 333  {{layout-section ac:type="single"}}
334 334  {{layout-cell}}
335 335  ----
336 336  
337 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
359 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
338 338  
339 339  * (((
340 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
362 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
341 341  
342 342  * Tape roll empty?
343 343  * motor connected (icon green)?
344 344  )))
345 345  
368 +\\
369 +
346 346  * (((
347 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
371 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
348 348  
349 349  * displayed in green=connected?
350 350  * nozzle holder colliding somewhere?
... ... @@ -351,8 +351,10 @@
351 351  * motor limits reached? → position displayed in red
352 352  )))
353 353  
378 +\\
379 +
354 354  * (((
355 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
381 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
356 356  
357 357  * channel turned on?
358 358  * Sample empty?
... ... @@ -359,21 +359,20 @@
359 359  * Nozzle or lines clogged? → flush with water, change nozzle
360 360  )))
361 361  
388 +\\
389 +
362 362  * (((
363 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
391 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
364 364  
365 365  * First, restart kamzik (server+client) and see if this solves the issue
366 366  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
367 367  * (((
368 -If nothing works, kill the Simplon process and then start the server again:*
369 -
370 -(((
396 +If nothing works, kill the Simplon process and then start the server again:* (((
371 371  (% class="code" %)
372 372  (((
373 373  ssh haspp11exp03
374 374  )))
375 375  )))
376 -
377 377  * (((
378 378  (% class="code" %)
379 379  (((
... ... @@ -387,8 +387,13 @@
387 387  )))
388 388  )))
389 389  )))
390 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
391 391  )))
392 392  {{/layout-cell}}
393 393  {{/layout-section}}
418 +
419 +{{layout-section ac:type="single"}}
420 +{{layout-cell}}
421 +\\
422 +{{/layout-cell}}
423 +{{/layout-section}}
394 394  {{/layout}}
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