Skip to Content
Last modified by chatzies on 2025-11-27 11:35
From version 76.1
edited by ahenkel
on 2022-11-02 16:25
Change comment: There is no comment for this version
To version 46.1
edited by ahenkel
on 2021-12-12 23:53
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -1,7 +1,7 @@
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  \\
7 7  
... ... @@ -9,22 +9,18 @@
9 9  
10 10  \\
11 11  
12 -----
13 -
14 14  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
15 15  
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.
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.
17 17  
18 18  Preparation:
19 19  
20 -* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
18 +* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
21 21  
22 22  [[image:attach:20211201_095534.jpg||height="250"]]
23 23  
24 24  \\
25 25  
26 -----
27 -
28 28  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 29  ** ==
30 30  
... ... @@ -44,8 +44,6 @@
44 44  
45 45  \\
46 46  
47 -----
48 -
49 49  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 50  ** ==
51 51  
... ... @@ -57,7 +57,7 @@
57 57  
58 58  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
59 59  
60 -* Click the 'main tape' icon
54 +* 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.
... ... @@ -66,7 +66,7 @@
66 66  
67 67  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
68 68  
69 -* Click on the 'nozzle' icon.
63 +* 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.
... ... @@ -145,10 +145,8 @@
145 145  
146 146  \\
147 147  
148 -----
142 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ==
149 149  
150 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
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  
154 154  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -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**. //!!!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.
... ... @@ -170,17 +170,15 @@
170 170  
171 171  \\
172 172  
173 -**
174 -**
165 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
166 +** ===
175 175  {{/layout-cell}}
176 176  {{/layout-section}}
177 177  
178 178  {{layout-section ac:type="single"}}
179 179  {{layout-cell}}
180 -----
172 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ==
181 181  
182 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183 -
184 184  start chopper gui from terminal:
185 185  
186 186  (% class="code" %)
... ... @@ -191,7 +191,6 @@
191 191  (% class="code" %)
192 192  (((
193 193   python chopperControl.py
194 -\\\\
195 195  )))
196 196  {{/layout-cell}}
197 197  {{/layout-section}}
... ... @@ -214,72 +214,76 @@
214 214  * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
215 215  * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
216 216  ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
217 -* (% style="color: rgb(0,0,0);" %)//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 -//
206 +* (% style="color: rgb(0,0,0);" %)//usually 133 Hz, results in exposure time of 3.7 ms//
219 219  {{/layout-cell}}
220 220  {{/layout-section}}
221 221  
222 222  {{layout-section ac:type="single"}}
223 223  {{layout-cell}}
224 -----
212 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ==
225 225  
226 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227 -
228 228  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
229 229  
230 230  (% class="code" %)
231 231  (((
232 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
218 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
233 233   password: written on control laptop (changes every 6 months)
234 234  )))
235 235  
236 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
222 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
237 237  
238 238  \\
225 +
226 +Click "Start" icon in kamzik.
227 +
228 +[[image:attach:kamzik_run-tile.jpg||height="400"]]
229 +
230 +----
239 239  {{/layout-cell}}
240 240  {{/layout-section}}
241 241  
242 -{{layout-section ac:type="two_left_sidebar"}}
234 +{{layout-section ac:type="two_equal"}}
243 243  {{layout-cell}}
244 244  **Check list:**
245 245  
246 246  (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
247 247  
248 -(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
240 +* Open BS1  (//CrystalControl)//
241 +* Put collimator in (//CrystalControl)//
242 +* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
243 +* Open fast shutter (//CrystalControl)//
244 +* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
245 +* Close fast shutter (//CrystalControl)//
249 249  
250 -* Put detector distance 200 in //prepare_for_measurement (      )
251 -//
252 -* Click "<Call>" next to //prepare_for_measurement
253 -//This will:\\
254 -** drive the collimator in //IN// position
255 -** drive detector to 200 mm
256 -
257 257  \\
258 258  
259 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
249 +**Set run parameters and go 🏃💥**
260 260  
251 +1. Set your desired No. of frames
252 +1. Match exposure time with chopper setting
253 +1. Check trigger setting and match to chopper setting
254 +1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
255 +1. To start the run, click "<Call>" next to //exposure time//
256 +
261 261  \\
262 262  
263 -//**Set run parameters and go 🏃💥**//
259 +(% style="color: rgb(153,51,102);" %)**//Current bug~://**
264 264  
265 -1. Set your desired No. of frames
266 -1. Enter the protein ID of your crystal sample
267 -1. Match exposure time with chopper setting or set desired exposure time
268 -1. Check trigger setting and match to chopper setting
269 -no chopper → external triffer //off
270 -// chopper → external trigger// on
271 -//
272 -1. To start the run, click "<Call>" next to //start_run (exposure    )//
273 -{{/layout-cell}}
261 +(% 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>".
274 274  
275 -{{layout-cell}}
276 -[[image:attach:Kamzik_run(2).PNG]]
263 +
264 +(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
265 +
266 +(% class="code" %)
267 +(((
268 + cd /gpfs/current/raw/scan_frames
269 + watch "ls -lrt <run number>/ | tail"
270 +\\\\\\\\
271 +)))
277 277  {{/layout-cell}}
278 -{{/layout-section}}
279 279  
280 -{{layout-section ac:type="single"}}
281 281  {{layout-cell}}
282 -(% class="relative-table wrapped" style="width: 55.9569%;" %)
275 +(% class="wrapped relative-table" style="width: 100.0%;" %)
283 283  |=(((
284 284  Parameter
285 285  )))|=(((
... ... @@ -290,7 +290,7 @@
290 290  |(((
291 291  Images number
292 292  )))|(((
293 -number of frames you want to collect
286 +Set number of frames you want to collect
294 294  )))|(% colspan="1" %)(((
295 295  usually 100k - 200k, but adjust according to hitrate
296 296  
... ... @@ -303,7 +303,10 @@
303 303  
304 304  \\
305 305  )))|(% colspan="1" %)(((
306 -with chopper         → opening time displayed in chopper GUI
299 +chopper at 133 Hz → 3.7 ms
300 +
301 +chopper at 66 Hz   → 7.7 ms
302 +
307 307  no chopper            → 7.7 ms
308 308  
309 309  ----
... ... @@ -323,50 +323,29 @@
323 323  \\
324 324  )))
325 325  |(% colspan="1" %)(((
326 -protein ID
322 +move_detector (distance)
327 327  )))|(% colspan="1" %)(((
328 -protein ID of crystal sample (see AMARCORD)
324 +Set detector distance
329 329  )))|(% colspan="1" %)(((
330 -\\
326 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
331 331  )))
332 -
333 -----
328 +|(% colspan="1" %)(((
329 +Diode voltage
330 +)))|(% colspan="1" %)(((
331 +read out of diode
332 +)))|(% colspan="1" %)(((
333 +**~~ 0 !!! higher values indicate missaligned beam stop!!! 
334 +Call local contact
335 +**
336 +)))
334 334  {{/layout-cell}}
335 335  {{/layout-section}}
336 336  
337 -{{layout-section ac:type="two_equal"}}
338 -{{layout-cell}}
339 -**After data collection/Before entering the exp. hutch:**
340 -
341 -1. Go to "Safety" in kamzik.
342 -1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
343 -11. Drive the collimator out
344 -11. Drive the detector back to 1500 mm
345 -1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
346 -
347 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
348 -{{/layout-cell}}
349 -
350 -{{layout-cell}}
351 -\\
352 -
353 -\\
354 -
355 -\\
356 -
357 -\\
358 -
359 -\\
360 -
361 -[[image:attach:safety_kamzik.PNG]]
362 -{{/layout-cell}}
363 -{{/layout-section}}
364 -
365 365  {{layout-section ac:type="single"}}
366 366  {{layout-cell}}
367 367  ----
368 368  
369 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
344 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}**14.9 Troubleshooting** ==
370 370  
371 371  * (((
372 372  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -394,42 +394,6 @@
394 394  * Sample empty?
395 395  * Nozzle or lines clogged? → flush with water, change nozzle
396 396  )))
397 -
398 -\\
399 -
400 -* (((
401 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
402 -
403 -* First, restart kamzik (server+client) and see if this solves the issue
404 -* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
405 -* (((
406 -If nothing works, kill the Simplon process and then start the server again:* (((
407 -(% class="code" %)
408 -(((
409 -ssh haspp11exp03
410 -)))
411 -)))
412 -* (((
413 -(% class="code" %)
414 -(((
415 -ps -ef | grep Simplon
416 -)))
417 -)))
418 -* (((
419 -(% class="code" %)
420 -(((
421 -kill -9 simplon_process_id
422 -)))
423 -)))
424 -)))
425 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
426 -)))
427 427  {{/layout-cell}}
428 428  {{/layout-section}}
429 -
430 -{{layout-section ac:type="single"}}
431 -{{layout-cell}}
432 -\\
433 -{{/layout-cell}}
434 -{{/layout-section}}
435 435  {{/layout}}
20211201_094101.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -5.8 MB
Content
20211201_094111.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -5.6 MB
Content
20211201_095033.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -3.1 MB
Content
20211201_095205.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -2.8 MB
Content
20211201_095232.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -7.2 MB
Content
20211201_095534.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -4.4 MB
Content
20211212_233140.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -6.5 MB
Content
Kamzik_run(2).PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -134.4 KB
Content
Screenshot from 2022-04-04 19-36-29.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -133.0 KB
Content
TapeDrive coords.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -24.1 KB
Content
TapeDrive scheme.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -114.3 KB
Content
TapeDrive_beschriftet-tile.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -539.9 KB
Content
TapeDrive_beschriftet.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -337.8 KB
Content
kamzik_nozzle.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -120.5 KB
Content
kamzik_run-tile.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -466.4 KB
Content
kamzik_run.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -128.9 KB
Content
kamzik_safety.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -139.1 KB
Content
kamzik_tape.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -122.6 KB
Content
safety_kamzik.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -126.9 KB
Content
screen.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -94.0 KB
Content
server client.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -262.2 KB
Content
tape reset.PNG
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
Size
... ... @@ -1,1 +1,0 @@
1 -122.3 KB
Content
Confluence.Code.ConfluencePageClass[0]
Id
... ... @@ -1,1 +1,1 @@
1 -235031805
1 +236824598
URL
... ... @@ -1,1 +1,1 @@
1 -https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/236824598/14. Serial Crystallography: CFEL TapeDrive