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From version 45.1
edited by ahenkel
on 2021-12-12 23:53
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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
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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 -\\
7 +{{toc minLevel="2"/}}
9 9  
10 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
11 11  
12 -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.
10 +----
13 13  
12 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**8.1 Sample characteristics and preparation** ==
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.
15 +
14 14  Preparation:
15 15  
16 -* 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
17 17  
18 18  [[image:attach:20211201_095534.jpg||height="250"]]
19 19  
20 -\\
21 21  
22 -== {{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"/}}**8.2 Connecting sample to ElveFlow, sample exchange** ==
26 +
27 +*
23 23  ** ==
24 24  
25 25  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!**
... ... @@ -36,12 +36,15 @@
36 36  
37 37  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
38 38  
39 -\\
40 40  
41 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
45 +----
46 +
47 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**8.3 TapeDrive operation** ==
48 +
49 +*
42 42  ** ==
43 43  
44 -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.
45 45  Now start the client. Same thing, a terminal will open, shortly after a small window.
46 46  
47 47  Click 'Devices' in the **client session** to open the control window.
... ... @@ -49,31 +49,31 @@
49 49  
50 50  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
51 51  
52 -* Click on the 'main tape' icon
60 +* Click the 'main tape' icon
53 53  * Change the velocity by typing anything from **0.3-3.0 mm/s**
54 54  * Common velocity is 1.0-1.5 mm/s
55 55  * 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.
56 -\\
64 +
57 57  * [[image:attach:kamzik_tape.PNG||height="400"]]
58 58  
59 59  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
60 60  
61 -* Click an the 'nozzle' icon.
69 +* Click on the 'nozzle' icon.
62 62  * (((
63 63  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.
64 64  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
65 65  
66 66  
67 -(% 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" %)** !!!**(%%)
68 68  \\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.
69 69  
70 70  (% class="wrapped" %)
71 71  |=(((
72 -\\
80 +
73 73  )))|=(((
74 74  direction
75 75  )))|=(((
76 -recommended step size
84 +recommended step size
77 77  for visual adjustment
78 78  )))|=(% colspan="1" %)(((
79 79  recommended step size
... ... @@ -108,8 +108,7 @@
108 108  be careful with -z, tape could be pushed out of focus
109 109  )))
110 110  
111 -**
112 -\\**
119 +
113 113  )))
114 114  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
115 115  
... ... @@ -117,28 +117,23 @@
117 117  
118 118  * The chiller circulates fluid through the gas nozzle.
119 119  
120 -\\
121 -
122 122  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
123 123  
124 -\\
125 125  
126 126  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
127 127  
128 -\\
129 129  
130 130  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
131 131  
132 132   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
133 - password: //written on control laptop (changes every 6 months)
134 -//
136 + password: //written on control laptop (changes every 6 months)//
135 135  
136 -\\
137 137  
138 -\\
139 139  
140 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ==
140 +----
141 141  
142 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**8.4 Tape roll exchange** ==
143 +
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  
144 144  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -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**. //!!!BEAMSTOP!!!//
151 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!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.
... ... @@ -153,32 +153,31 @@
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"]]
157 -**
158 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
158 158  
159 -\\
160 160  
161 -\\
162 162  
163 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
164 -** ===
162 +
165 165  {{/layout-cell}}
166 166  {{/layout-section}}
167 167  
168 168  {{layout-section ac:type="single"}}
169 169  {{layout-cell}}
170 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ==
168 +----
171 171  
170 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**8.5 Chopper** ==
171 +
172 172  start chopper gui from terminal:
173 173  
174 174  (% class="code" %)
175 175  (((
176 - cd /gpfs/local/shared/ChopperControl
176 + cd /gpfs/local/shared/ChopperControl          
177 177  )))
178 178  
179 179  (% class="code" %)
180 180  (((
181 181   python chopperControl.py
182 +\\
182 182  )))
183 183  {{/layout-cell}}
184 184  {{/layout-section}}
... ... @@ -191,86 +191,75 @@
191 191  {{layout-cell}}
192 192  **Chopper → no Chopper**
193 193  
194 -* decrease frequency by max. 10 Hz steps\\
195 +* decrease frequency by max. 10 Hz steps
195 195  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
196 196  * at frequency = 10 Hz, click "Stop"
197 -* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
198 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
198 198  
199 -(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
200 +(% style="color:#000000" %)**no Chopper → Chopper**
200 200  
201 -* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
202 -* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
203 -** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
204 -* (% 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//
205 205  {{/layout-cell}}
206 206  {{/layout-section}}
207 207  
208 208  {{layout-section ac:type="single"}}
209 209  {{layout-cell}}
210 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ==
211 +----
211 211  
213 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**8.6 Data collection** ==
214 +
212 212  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
213 213  
214 214  (% class="code" %)
215 215  (((
216 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
219 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
217 217   password: written on control laptop (changes every 6 months)
218 218  )))
219 219  
220 - //>>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//
221 221  
222 -\\
223 -
224 -Click "Start" icon in kamzik.
225 -
226 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
227 -
228 -----
225 +
229 229  {{/layout-cell}}
230 230  {{/layout-section}}
231 231  
232 -{{layout-section ac:type="two_equal"}}
229 +{{layout-section ac:type="two_left_sidebar"}}
233 233  {{layout-cell}}
234 234  **Check list:**
235 235  
236 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
233 +(% style="color:#ff0000" %)//always after entering the hutch!//
237 237  
238 -* Open BS1  (//CrystalControl)//
239 -* Put collimator in (//CrystalControl)//
240 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
241 -* Open fast shutter (//CrystalControl)//
242 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
243 -* Close fast shutter (//CrystalControl)//
235 +(% style="color:#000000" %)Click "Run" icon in kamzik.
244 244  
245 -\\
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
246 246  
247 -**Set run parameters and go 🏃💥**
243 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
248 248  
245 +//**Set run parameters and go 🏃💥**//
246 +
249 249  1. Set your desired No. of frames
250 -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
251 251  1. Check trigger setting and match to chopper setting
252 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
253 -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}}
254 254  
255 -\\
256 -
257 -(% style="color: rgb(153,51,102);" %)**//Current bug~://**
258 -
259 -(% 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>".
260 -
261 -
262 -(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
263 -
264 -(% class="code" %)
265 -(((
266 - cd /gpfs/current/raw/scan_frames
267 - watch "ls -lrt <run number>/ | tail"
268 -\\\\\\\\
269 -)))
256 +{{layout-cell}}
257 +[[image:attach:Kamzik_run(2).PNG]]
270 270  {{/layout-cell}}
259 +{{/layout-section}}
271 271  
261 +{{layout-section ac:type="single"}}
272 272  {{layout-cell}}
273 -(% class="wrapped relative-table" style="width: 100.0%;" %)
263 +(% class="relative-table wrapped" style="width:55.9569%" %)
274 274  |=(((
275 275  Parameter
276 276  )))|=(((
... ... @@ -281,7 +281,7 @@
281 281  |(((
282 282  Images number
283 283  )))|(((
284 -Set number of frames you want to collect
274 +number of frames you want to collect
285 285  )))|(% colspan="1" %)(((
286 286  usually 100k - 200k, but adjust according to hitrate
287 287  
... ... @@ -292,12 +292,9 @@
292 292  )))|(((
293 293  exposure time of Eiger
294 294  
295 -\\
285 +
296 296  )))|(% colspan="1" %)(((
297 -chopper at 133 Hz → 3.7 ms
298 -
299 -chopper at 66 Hz   → 7.7 ms
300 -
287 +with chopper         → opening time displayed in chopper GUI
301 301  no chopper            → 7.7 ms
302 302  
303 303  ----
... ... @@ -307,7 +307,7 @@
307 307  )))|(((
308 308  changes automatically
309 309  )))|(% colspan="1" %)(((
310 -\\
297 +
311 311  )))
312 312  |(% colspan="1" %)(((
313 313  Detector distance
... ... @@ -314,32 +314,49 @@
314 314  )))|(% colspan="1" %)(((
315 315  current detector postion readout
316 316  )))|(% colspan="1" %)(((
317 -\\
304 +
318 318  )))
319 319  |(% colspan="1" %)(((
320 -move_detector (distance)
307 +protein ID
321 321  )))|(% colspan="1" %)(((
322 -Set detector distance
309 +protein ID of crystal sample (see AMARCORD)
323 323  )))|(% colspan="1" %)(((
324 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
311 +
325 325  )))
326 -|(% colspan="1" %)(((
327 -Diode voltage
328 -)))|(% colspan="1" %)(((
329 -read out of diode
330 -)))|(% colspan="1" %)(((
331 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 
332 -Call local contact
333 -**
334 -)))
313 +
314 +----
335 335  {{/layout-cell}}
336 336  {{/layout-section}}
337 337  
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 +
338 338  {{layout-section ac:type="single"}}
339 339  {{layout-cell}}
340 340  ----
341 341  
342 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}**14.9 Troubleshooting** ==
346 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**8.7 Troubleshooting** ==
343 343  
344 344  * (((
345 345  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -348,8 +348,6 @@
348 348  * motor connected (icon green)?
349 349  )))
350 350  
351 -\\
352 -
353 353  * (((
354 354  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
355 355  
... ... @@ -358,8 +358,6 @@
358 358  * motor limits reached? → position displayed in red
359 359  )))
360 360  
361 -\\
362 -
363 363  * (((
364 364  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
365 365  
... ... @@ -367,6 +367,43 @@
367 367  * Sample empty?
368 368  * Nozzle or lines clogged? → flush with water, change nozzle
369 369  )))
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 +)))
370 370  {{/layout-cell}}
371 371  {{/layout-section}}
403 +
404 +{{layout-section ac:type="single"}}
405 +{{layout-cell}}
406 +
407 +{{/layout-cell}}
408 +{{/layout-section}}
372 372  {{/layout}}
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