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Title
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1 -08. Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.tabermah
1 +XWiki.ahenkel
Content
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3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 7  {{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 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  
... ... @@ -19,12 +19,11 @@
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** ==
26 -
27 -*
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
28 28  ** ==
29 29  
30 30  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!**
... ... @@ -41,15 +41,14 @@
41 41  
42 42  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
43 43  
45 +\\
44 44  
45 45  ----
46 46  
47 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**8.3 TapeDrive operation** ==
48 -
49 -*
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
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:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving, 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);" %)** !!!**(%%)
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
... ... @@ -116,7 +116,8 @@
116 116  be careful with -z, tape could be pushed out of focus
117 117  )))
118 118  
119 -
119 +**
120 +\\**
120 120  )))
121 121  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
122 122  
... ... @@ -124,22 +124,29 @@
124 124  
125 125  * The chiller circulates fluid through the gas nozzle.
126 126  
128 +\\
129 +
127 127  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
128 128  
132 +\\
129 129  
130 130  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
131 131  
136 +\\
132 132  
133 133  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
134 134  
135 135   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
136 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
137 137  
144 +\\
138 138  
146 +\\
139 139  
140 140  ----
141 141  
142 -== {{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** ==
143 143  
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  
... ... @@ -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**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!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.
... ... @@ -155,11 +155,15 @@
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"]]**
166 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 +**
159 159  
169 +\\
160 160  
171 +\\
161 161  
162 -
173 +**
174 +**
163 163  {{/layout-cell}}
164 164  {{/layout-section}}
165 165  
... ... @@ -167,19 +167,19 @@
167 167  {{layout-cell}}
168 168  ----
169 169  
170 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**8.5 Chopper** ==
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
171 171  
172 172  start chopper gui from terminal:
173 173  
174 174  (% class="code" %)
175 175  (((
176 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
177 177  )))
178 178  
179 179  (% class="code" %)
180 180  (((
181 181   python chopperControl.py
182 -\\
194 +\\\\
183 183  )))
184 184  {{/layout-cell}}
185 185  {{/layout-section}}
... ... @@ -192,37 +192,36 @@
192 192  {{layout-cell}}
193 193  **Chopper → no Chopper**
194 194  
195 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
196 196  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
197 197  * at frequency = 10 Hz, click "Stop"
198 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
199 199  
200 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
201 201  
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//
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 +//
206 206  {{/layout-cell}}
207 207  {{/layout-section}}
208 208  
209 209  {{layout-section ac:type="single"}}
210 210  {{layout-cell}}
211 -----
224 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
212 212  
213 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**8.6 Data collection** ==
214 -
215 215  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
216 216  
217 217  (% class="code" %)
218 218  (((
219 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
230 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
220 220   password: written on control laptop (changes every 6 months)
221 221  )))
222 222  
223 223   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
224 224  
225 -
236 +\\
226 226  {{/layout-cell}}
227 227  {{/layout-section}}
228 228  
... ... @@ -230,37 +230,62 @@
230 230  {{layout-cell}}
231 231  **Check list:**
232 232  
233 -(% style="color:#ff0000" %)//always after entering the hutch!//
244 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
234 234  
235 -(% style="color:#000000" %)Click "Run" icon in kamzik.
246 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
236 236  
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 +* Put collimator in
249 +** Put detector distance 200 in //prepare_for_measurement (      )
250 +//
251 +** Click "<Call>" next to //prepare_for_measurement//
242 242  
243 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
253 +\\
244 244  
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    )//
255 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
254 254  {{/layout-cell}}
255 255  
256 256  {{layout-cell}}
257 -[[image:attach:Kamzik_run(2).PNG]]
259 +[[image:attach:kamzik_safety.PNG||height="400"]]
258 258  {{/layout-cell}}
259 259  {{/layout-section}}
260 260  
261 261  {{layout-section ac:type="single"}}
262 262  {{layout-cell}}
263 -(% 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%;" %)
264 264  |=(((
265 265  Parameter
266 266  )))|=(((
... ... @@ -271,7 +271,7 @@
271 271  |(((
272 272  Images number
273 273  )))|(((
274 -number of frames you want to collect
310 +Set number of frames you want to collect
275 275  )))|(% colspan="1" %)(((
276 276  usually 100k - 200k, but adjust according to hitrate
277 277  
... ... @@ -282,9 +282,12 @@
282 282  )))|(((
283 283  exposure time of Eiger
284 284  
285 -
321 +\\
286 286  )))|(% colspan="1" %)(((
287 -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 +
288 288  no chopper            → 7.7 ms
289 289  
290 290  ----
... ... @@ -294,7 +294,7 @@
294 294  )))|(((
295 295  changes automatically
296 296  )))|(% colspan="1" %)(((
297 -
336 +\\
298 298  )))
299 299  |(% colspan="1" %)(((
300 300  Detector distance
... ... @@ -301,49 +301,23 @@
301 301  )))|(% colspan="1" %)(((
302 302  current detector postion readout
303 303  )))|(% colspan="1" %)(((
304 -
343 +\\
305 305  )))
306 306  |(% colspan="1" %)(((
307 -protein ID
346 +move_detector (distance)
308 308  )))|(% colspan="1" %)(((
309 -protein ID of crystal sample (see AMARCORD)
348 +Set detector distance
310 310  )))|(% colspan="1" %)(((
311 -
350 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
312 312  )))
313 -
314 -----
315 315  {{/layout-cell}}
316 316  {{/layout-section}}
317 317  
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 -
342 342  {{layout-section ac:type="single"}}
343 343  {{layout-cell}}
344 344  ----
345 345  
346 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**8.7 Troubleshooting** ==
359 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
347 347  
348 348  * (((
349 349  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -352,6 +352,8 @@
352 352  * motor connected (icon green)?
353 353  )))
354 354  
368 +\\
369 +
355 355  * (((
356 356  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
357 357  
... ... @@ -360,6 +360,8 @@
360 360  * motor limits reached? → position displayed in red
361 361  )))
362 362  
378 +\\
379 +
363 363  * (((
364 364  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
365 365  
... ... @@ -368,6 +368,8 @@
368 368  * Nozzle or lines clogged? → flush with water, change nozzle
369 369  )))
370 370  
388 +\\
389 +
371 371  * (((
372 372  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
373 373  
... ... @@ -374,15 +374,12 @@
374 374  * First, restart kamzik (server+client) and see if this solves the issue
375 375  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
376 376  * (((
377 -If nothing works, kill the Simplon process and then start the server again:*
378 -
379 -(((
396 +If nothing works, kill the Simplon process and then start the server again:* (((
380 380  (% class="code" %)
381 381  (((
382 382  ssh haspp11exp03
383 383  )))
384 384  )))
385 -
386 386  * (((
387 387  (% class="code" %)
388 388  (((
... ... @@ -396,7 +396,6 @@
396 396  )))
397 397  )))
398 398  )))
399 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
400 400  )))
401 401  {{/layout-cell}}
402 402  {{/layout-section}}
... ... @@ -403,7 +403,7 @@
403 403  
404 404  {{layout-section ac:type="single"}}
405 405  {{layout-cell}}
406 -
421 +\\
407 407  {{/layout-cell}}
408 408  {{/layout-section}}
409 409  {{/layout}}
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