Skip to Content
Last modified by chatzies on 2025-11-27 11:35
From version 47.1
edited by ahenkel
on 2021-12-12 23:57
Change comment: There is no comment for this version
To version 76.1
edited by ahenkel
on 2022-11-02 16:25
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="250"]]
4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 6  \\
7 7  
... ... @@ -13,11 +13,11 @@
13 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.
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  
18 18  Preparation:
19 19  
20 -* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube
20 +* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
21 21  
22 22  [[image:attach:20211201_095534.jpg||height="250"]]
23 23  
... ... @@ -57,7 +57,7 @@
57 57  
58 58  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
59 59  
60 -* Click on the 'main tape' icon
60 +* Click 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 an the 'nozzle' icon.
69 +* Click on 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.
... ... @@ -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**. //!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!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.
... ... @@ -170,8 +170,8 @@
170 170  
171 171  \\
172 172  
173 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}**
174 -** ===
173 +**
174 +**
175 175  {{/layout-cell}}
176 176  {{/layout-section}}
177 177  
... ... @@ -214,7 +214,8 @@
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 133 Hz, results in exposure time of 3.7 ms//
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 +//
218 218  {{/layout-cell}}
219 219  {{/layout-section}}
220 220  
... ... @@ -228,64 +228,57 @@
228 228  
229 229  (% class="code" %)
230 230  (((
231 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
232 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
232 232   password: written on control laptop (changes every 6 months)
233 233  )))
234 234  
235 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
236 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
236 236  
237 237  \\
238 -
239 -Click "Start" icon in kamzik.
240 -
241 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
242 -
243 -----
244 244  {{/layout-cell}}
245 245  {{/layout-section}}
246 246  
247 -{{layout-section ac:type="two_equal"}}
242 +{{layout-section ac:type="two_left_sidebar"}}
248 248  {{layout-cell}}
249 249  **Check list:**
250 250  
251 251  (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
252 252  
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)//
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
259 259  
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 +
260 260  \\
261 261  
262 -**Set run parameters and go 🏃💥**
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
263 263  
264 -1. Set your desired No. of frames
265 -1. Match exposure time with chopper setting
266 -1. Check trigger setting and match to chopper setting
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//
269 -
270 270  \\
271 271  
272 -(% style="color: rgb(153,51,102);" %)**//Current bug~://**
263 +//**Set run parameters and go 🏃💥**//
273 273  
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>".
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}}
275 275  
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 -)))
275 +{{layout-cell}}
276 +[[image:attach:Kamzik_run(2).PNG]]
285 285  {{/layout-cell}}
278 +{{/layout-section}}
286 286  
280 +{{layout-section ac:type="single"}}
287 287  {{layout-cell}}
288 -(% class="wrapped relative-table" style="width: 100.0%;" %)
282 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
289 289  |=(((
290 290  Parameter
291 291  )))|=(((
... ... @@ -296,7 +296,7 @@
296 296  |(((
297 297  Images number
298 298  )))|(((
299 -Set number of frames you want to collect
293 +number of frames you want to collect
300 300  )))|(% colspan="1" %)(((
301 301  usually 100k - 200k, but adjust according to hitrate
302 302  
... ... @@ -309,10 +309,7 @@
309 309  
310 310  \\
311 311  )))|(% colspan="1" %)(((
312 -chopper at 133 Hz → 3.7 ms
313 -
314 -chopper at 66 Hz   → 7.7 ms
315 -
306 +with chopper         → opening time displayed in chopper GUI
316 316  no chopper            → 7.7 ms
317 317  
318 318  ----
... ... @@ -332,24 +332,45 @@
332 332  \\
333 333  )))
334 334  |(% colspan="1" %)(((
335 -move_detector (distance)
326 +protein ID
336 336  )))|(% colspan="1" %)(((
337 -Set detector distance
328 +protein ID of crystal sample (see AMARCORD)
338 338  )))|(% colspan="1" %)(((
339 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
330 +\\
340 340  )))
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 -)))
332 +
333 +----
350 350  {{/layout-cell}}
351 351  {{/layout-section}}
352 352  
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 +
353 353  {{layout-section ac:type="single"}}
354 354  {{layout-cell}}
355 355  ----
... ... @@ -382,6 +382,42 @@
382 382  * Sample empty?
383 383  * Nozzle or lines clogged? → flush with water, change nozzle
384 384  )))
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 +)))
385 385  {{/layout-cell}}
386 386  {{/layout-section}}
429 +
430 +{{layout-section ac:type="single"}}
431 +{{layout-cell}}
432 +\\
433 +{{/layout-cell}}
434 +{{/layout-section}}
387 387  {{/layout}}
20211201_094101.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +5.8 MB
Content
20211201_094111.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +5.6 MB
Content
20211201_095033.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +3.1 MB
Content
20211201_095205.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +2.8 MB
Content
20211201_095232.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +7.2 MB
Content
20211201_095534.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +4.4 MB
Content
20211212_233140.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +6.5 MB
Content
Kamzik_run(2).PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +134.4 KB
Content
Screenshot from 2022-04-04 19-36-29.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +133.0 KB
Content
TapeDrive coords.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +24.1 KB
Content
TapeDrive scheme.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +114.3 KB
Content
TapeDrive_beschriftet-tile.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +539.9 KB
Content
TapeDrive_beschriftet.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +337.8 KB
Content
kamzik_nozzle.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +120.5 KB
Content
kamzik_run-tile.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +466.4 KB
Content
kamzik_run.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +128.9 KB
Content
kamzik_safety.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +139.1 KB
Content
kamzik_tape.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +122.6 KB
Content
safety_kamzik.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +126.9 KB
Content
screen.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +94.0 KB
Content
server client.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +262.2 KB
Content
tape reset.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +122.3 KB
Content
Confluence.Code.ConfluencePageClass[0]
Id
... ... @@ -1,1 +1,1 @@
1 -236824604
1 +235031805
URL
... ... @@ -1,1 +1,1 @@
1 -https://confluence.desy.de/spaces/11/pages/236824604/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive