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Last modified by chatzies on 2025-11-27 11:35
From version 78.1
edited by tabermah
on 2024-12-03 11:34
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To version 47.1
edited by ahenkel
on 2021-12-12 23:57
Change comment: There is no comment for this version

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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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1 1  {{layout}}
2 2  {{layout-section ac:type="single"}}
3 3  {{layout-cell}}
4 -[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
5 5  
6 +\\
6 6  
7 7  {{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 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.
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 cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
20 +* filter through 30 µm cell filter (green) 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"/}}**14.2 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"/}}**14.3 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.
... ... @@ -57,31 +57,31 @@
57 57  
58 58  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
59 59  
60 -* Click the 'main tape' icon
60 +* Click on the 'main tape' icon
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** ====
68 68  
69 -* Click on the 'nozzle' icon.
69 +* Click an the 'nozzle' icon.
70 70  * (((
71 71  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.
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  
... ... @@ -124,18 +124,25 @@
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  
... ... @@ -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**. //!!!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 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
174 +** ===
163 163  {{/layout-cell}}
164 164  {{/layout-section}}
165 165  
... ... @@ -173,13 +173,13 @@
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}}
... ... @@ -192,17 +192,17 @@
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//
206 206  {{/layout-cell}}
207 207  {{/layout-section}}
208 208  
... ... @@ -216,51 +216,64 @@
216 216  
217 217  (% class="code" %)
218 218  (((
219 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
231 + 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 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
235 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
224 224  
225 -
237 +\\
238 +
239 +Click "Start" icon in kamzik.
240 +
241 +[[image:attach:kamzik_run-tile.jpg||height="400"]]
242 +
243 +----
226 226  {{/layout-cell}}
227 227  {{/layout-section}}
228 228  
229 -{{layout-section ac:type="two_left_sidebar"}}
247 +{{layout-section ac:type="two_equal"}}
230 230  {{layout-cell}}
231 231  **Check list:**
232 232  
233 -(% style="color:#ff0000" %)//always after entering the hutch!//
251 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
234 234  
235 -(% style="color:#000000" %)Click "Run" icon in kamzik.
253 +* Open BS1  (//CrystalControl)//
254 +* Put collimator in (//CrystalControl)//
255 +* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
256 +* Open fast shutter (//CrystalControl)//
257 +* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
258 +* Close fast shutter (//CrystalControl)//
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
260 +\\
242 242  
243 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
262 +**Set run parameters and go 🏃💥**
244 244  
245 -//**Set run parameters and go 🏃💥**//
246 -
247 247  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
265 +1. Match exposure time with chopper setting
250 250  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    )//
254 -{{/layout-cell}}
267 +1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
268 +1. To start the run, click "<Call>" next to //exposure time//
255 255  
256 -{{layout-cell}}
257 -[[image:attach:Kamzik_run(2).PNG]]
270 +\\
271 +
272 +(% style="color: rgb(153,51,102);" %)**//Current bug~://**
273 +
274 +(% 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>".
275 +
276 +
277 +(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
278 +
279 +(% class="code" %)
280 +(((
281 + cd /gpfs/current/raw/scan_frames
282 + watch "ls -lrt <run number>/ | tail"
283 +\\\\\\\\
284 +)))
258 258  {{/layout-cell}}
259 -{{/layout-section}}
260 260  
261 -{{layout-section ac:type="single"}}
262 262  {{layout-cell}}
263 -(% class="relative-table wrapped" style="width:55.9569%" %)
288 +(% 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
299 +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 -
310 +\\
286 286  )))|(% colspan="1" %)(((
287 -with chopper         → opening time displayed in chopper GUI
312 +chopper at 133 Hz → 3.7 ms
313 +
314 +chopper at 66 Hz   → 7.7 ms
315 +
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 -
325 +\\
298 298  )))
299 299  |(% colspan="1" %)(((
300 300  Detector distance
... ... @@ -301,44 +301,27 @@
301 301  )))|(% colspan="1" %)(((
302 302  current detector postion readout
303 303  )))|(% colspan="1" %)(((
304 -
332 +\\
305 305  )))
306 306  |(% colspan="1" %)(((
307 -protein ID
335 +move_detector (distance)
308 308  )))|(% colspan="1" %)(((
309 -protein ID of crystal sample (see AMARCORD)
337 +Set detector distance
310 310  )))|(% colspan="1" %)(((
311 -
339 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
312 312  )))
313 -
314 -----
341 +|(% colspan="1" %)(((
342 +Diode voltage
343 +)))|(% colspan="1" %)(((
344 +read out of diode
345 +)))|(% colspan="1" %)(((
346 +**~~ 0 !!! higher values indicate missaligned beam stop!!! 
347 +Call local contact
348 +**
349 +)))
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  ----
... ... @@ -352,6 +352,8 @@
352 352  * motor connected (icon green)?
353 353  )))
354 354  
366 +\\
367 +
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  
376 +\\
377 +
363 363  * (((
364 364  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
365 365  
... ... @@ -367,43 +367,6 @@
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 -)))
401 401  {{/layout-cell}}
402 402  {{/layout-section}}
403 -
404 -{{layout-section ac:type="single"}}
405 -{{layout-cell}}
406 -
407 -{{/layout-cell}}
408 -{{/layout-section}}
409 409  {{/layout}}
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1 -https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/236824604/14. Serial Crystallography: CFEL TapeDrive