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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
... ... @@ -3,15 +3,13 @@
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 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
12 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**8.1 Sample characteristics and preparation** ==
15 15  
16 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.
17 17  
... ... @@ -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"/}}**8.2 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"/}}**8.3 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 +116,7 @@
116 116  be careful with -z, tape could be pushed out of focus
117 117  )))
118 118  
119 -**
120 -\\**
119 +
121 121  )))
122 122  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
123 123  
... ... @@ -125,29 +125,22 @@
125 125  
126 126  * The chiller circulates fluid through the gas nozzle.
127 127  
128 -\\
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 -//
136 + password: //written on control laptop (changes every 6 months)//
143 143  
144 -\\
145 145  
146 -\\
147 147  
148 148  ----
149 149  
150 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
142 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**8.4 Tape roll exchange** ==
151 151  
152 152  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).
153 153  
... ... @@ -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!!!//
151 +* 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 -**
158 +**[[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 -**
162 +
175 175  {{/layout-cell}}
176 176  {{/layout-section}}
177 177  
... ... @@ -179,19 +179,19 @@
179 179  {{layout-cell}}
180 180  ----
181 181  
182 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
170 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**8.5 Chopper** ==
183 183  
184 184  start chopper gui from terminal:
185 185  
186 186  (% class="code" %)
187 187  (((
188 - cd /gpfs/local/shared/ChopperControl
176 + cd /gpfs/local/shared/ChopperControl          
189 189  )))
190 190  
191 191  (% class="code" %)
192 192  (((
193 193   python chopperControl.py
194 -\\\\
182 +\\
195 195  )))
196 196  {{/layout-cell}}
197 197  {{/layout-section}}
... ... @@ -204,35 +204,37 @@
204 204  {{layout-cell}}
205 205  **Chopper → no Chopper**
206 206  
207 -* decrease frequency by max. 10 Hz steps\\
195 +* 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//
198 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
211 211  
212 -(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
200 +(% 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//
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//
218 218  {{/layout-cell}}
219 219  {{/layout-section}}
220 220  
221 221  {{layout-section ac:type="single"}}
222 222  {{layout-cell}}
223 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
211 +----
224 224  
213 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**8.6 Data collection** ==
214 +
225 225  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
226 226  
227 227  (% class="code" %)
228 228  (((
229 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
219 + 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 -\\
225 +
236 236  {{/layout-cell}}
237 237  {{/layout-section}}
238 238  
... ... @@ -240,62 +240,37 @@
240 240  {{layout-cell}}
241 241  **Check list:**
242 242  
243 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
233 +(% style="color:#ff0000" %)//always after entering the hutch!//
244 244  
245 -(% style="color: rgb(0,0,0);" %)Click "Safety" icon in kamzik.
235 +(% style="color:#000000" %)Click "Run" icon in kamzik.
246 246  
247 -* Put collimator in
248 -** Click "<Call>" next to //collimator_in//
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
249 249  
250 -\\
243 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
251 251  
252 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
245 +//**Set run parameters and go 🏃💥**//
246 +
247 +1. Set your desired No. of frames
248 +1. Enter the protein ID of your crystal sample
249 +1. Match exposure time with chopper setting or set desired exposure time
250 +1. Check trigger setting and match to chopper setting
251 +no chopper → external triffer //off//
252 + chopper → external trigger// on//
253 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
253 253  {{/layout-cell}}
254 254  
255 255  {{layout-cell}}
256 -[[image:attach:kamzik_safety.PNG||height="400"]]
257 +[[image:attach:Kamzik_run(2).PNG]]
257 257  {{/layout-cell}}
258 258  {{/layout-section}}
259 259  
260 260  {{layout-section ac:type="single"}}
261 261  {{layout-cell}}
262 -----
263 -
264 -Click "Start/Run" icon in kamzik.
265 -
266 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
267 -
268 -----
269 -{{/layout-cell}}
270 -{{/layout-section}}
271 -
272 -{{layout-section ac:type="two_equal"}}
273 -{{layout-cell}}
274 -**Set run parameters and go 🏃💥**
275 -
276 -1. Set your desired No. of frames
277 -1. Match exposure time with chopper setting
278 -1. Check trigger setting and match to chopper setting
279 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
280 -1. To start the run, click "<Call>" next to //exposure time//
281 -
282 -\\
283 -
284 -\\
285 -
286 -**After data collection/Before entering the exp. hutch:**
287 -
288 -1. Go to "Safety" in kamzik.
289 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
290 -11. Drive the collimator out
291 -11. Drive the detector back to 1500 mm
292 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
293 -
294 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
295 -{{/layout-cell}}
296 -
297 -{{layout-cell}}
298 -(% class="wrapped relative-table" style="width: 100.0%;" %)
263 +(% class="relative-table wrapped" style="width:55.9569%" %)
299 299  |=(((
300 300  Parameter
301 301  )))|=(((
... ... @@ -306,7 +306,7 @@
306 306  |(((
307 307  Images number
308 308  )))|(((
309 -Set number of frames you want to collect
274 +number of frames you want to collect
310 310  )))|(% colspan="1" %)(((
311 311  usually 100k - 200k, but adjust according to hitrate
312 312  
... ... @@ -317,12 +317,9 @@
317 317  )))|(((
318 318  exposure time of Eiger
319 319  
320 -\\
285 +
321 321  )))|(% colspan="1" %)(((
322 -chopper at 133 Hz → 3.7 ms
323 -
324 -chopper at 66 Hz   → 7.7 ms
325 -
287 +with chopper         → opening time displayed in chopper GUI
326 326  no chopper            → 7.7 ms
327 327  
328 328  ----
... ... @@ -332,7 +332,7 @@
332 332  )))|(((
333 333  changes automatically
334 334  )))|(% colspan="1" %)(((
335 -\\
297 +
336 336  )))
337 337  |(% colspan="1" %)(((
338 338  Detector distance
... ... @@ -339,23 +339,49 @@
339 339  )))|(% colspan="1" %)(((
340 340  current detector postion readout
341 341  )))|(% colspan="1" %)(((
342 -\\
304 +
343 343  )))
344 344  |(% colspan="1" %)(((
345 -move_detector (distance)
307 +protein ID
346 346  )))|(% colspan="1" %)(((
347 -Set detector distance
309 +protein ID of crystal sample (see AMARCORD)
348 348  )))|(% colspan="1" %)(((
349 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
311 +
350 350  )))
313 +
314 +----
351 351  {{/layout-cell}}
352 352  {{/layout-section}}
353 353  
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 +
354 354  {{layout-section ac:type="single"}}
355 355  {{layout-cell}}
356 356  ----
357 357  
358 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
346 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**8.7 Troubleshooting** ==
359 359  
360 360  * (((
361 361  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -364,8 +364,6 @@
364 364  * motor connected (icon green)?
365 365  )))
366 366  
367 -\\
368 -
369 369  * (((
370 370  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
371 371  
... ... @@ -374,8 +374,6 @@
374 374  * motor limits reached? → position displayed in red
375 375  )))
376 376  
377 -\\
378 -
379 379  * (((
380 380  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
381 381  
... ... @@ -384,8 +384,6 @@
384 384  * Nozzle or lines clogged? → flush with water, change nozzle
385 385  )))
386 386  
387 -\\
388 -
389 389  * (((
390 390  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
391 391  
... ... @@ -392,12 +392,15 @@
392 392  * First, restart kamzik (server+client) and see if this solves the issue
393 393  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
394 394  * (((
395 -If nothing works, kill the Simplon process and then start the server again:* (((
377 +If nothing works, kill the Simplon process and then start the server again:*
378 +
379 +(((
396 396  (% class="code" %)
397 397  (((
398 398  ssh haspp11exp03
399 399  )))
400 400  )))
385 +
401 401  * (((
402 402  (% class="code" %)
403 403  (((
... ... @@ -411,6 +411,7 @@
411 411  )))
412 412  )))
413 413  )))
399 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
414 414  )))
415 415  {{/layout-cell}}
416 416  {{/layout-section}}
... ... @@ -417,7 +417,7 @@
417 417  
418 418  {{layout-section ac:type="single"}}
419 419  {{layout-cell}}
420 -\\
406 +
421 421  {{/layout-cell}}
422 422  {{/layout-section}}
423 423  {{/layout}}
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