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Last modified by chatzies on 2025-11-27 11:35
From version 43.1
edited by ahenkel
on 2021-12-12 23:49
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

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5 5  
6 6  \\
7 7  
8 -\\
8 +{{toc minLevel="2"/}}
9 9  
10 10  \\
11 11  
12 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
12 +----
13 13  
14 -* remove vortex
15 -* beamstop to out-position?
16 -* remove goniometer. The airbearing should be stopped (p11/servermotor/eh.1.01)
17 -* move cryojet out of the way, ramp the cryo up and shut it down. Close the compressed air to the shield flow. The biggest cable kinks and needs to be disconnected.
18 -* stop refill of the robot dewar and empty the dewar, warm up.
19 -* Disable backlight (unplug Festo connection). (% style="color: rgb(255,0,0);" %)//Is this still needed?//
20 -* (% style="color: rgb(0,0,0);" %)mount the 10 um diode and connect (via connector on the granite). This is connected to the leftmost Keithly (power up, check that settings are gain E06, Filter on, Rise time 1 ms. Keithly is connected to the oscilloscope and the delay generator, delay generator is connected to oscilloscope and detector, see diagram in P11 wiki. (% style="color: rgb(0, 0, 0); color: rgb(255, 0, 0)" %)//Insert here the setting for oscilloscope//(% style="color: rgb(0,0,0);" %)//. //Make sure to connect the multi-trigger to the back of the detector instead of the standard trigger, when starting to use the chopper (pull the thin ring with ‘grip’ area to detach). Cables are labeled. Make sure before using the chopper that the channels are enabled.
21 -* (% style="color: rgb(0,0,0);" %)move goniotower to X ~~ 17 000
14 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
22 22  
23 -(% style="color: rgb(0,0,0);" %)Mounting of the TapeDrive is done by the CFEL group. Electronics and control units are combined on a small shelf, that requires only one power and network plug-in. The shelf will be placed left-sided (looking upstream) to the detector tower. The ElveFlow and control laptop as well as several necessary consumables are placed on a cart, which is to be positioned on the right (looking upstream) against the robot platform. The CFEL chiller is placed on the right of the platform and connected to the TapeDrive GASnozzle.
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.
24 24  
25 -\\
26 -
27 -* adjust focus of the tape by moving X in goniometer tower until you see it in the overview camera. Final adjustment should be done when there is flow. Latest value is about 4500 in X and also 5000 in Z (higher soft limit changed from 2976,63 to 6000). (% style="color: rgb(255,0,0);" %)//Better to use the back illumination in the GUI to focus the tape - old instruction, not sure if this is the case. Back illumination is the external light source in the detector tower (the crystallography backlight should be disable for tapedrive).//
28 -* (% style="color: rgb(0,0,0);" %)Check the Minimum Detector Distance; the detector should not collide with the tapedrive while driven to 154 mm but it has to be verified. Also check that all cables and capillaries are taped away when the users start, so that nothing protrudes further than the tapedrive itself. Soft limit can be edited in eh.3.11 Atk panel.
29 -* (% style="color: rgb(0,0,0);" %)Reconfirm the alignment of the beamstop, once everything, including the nozzle, is in place. Modify config.ini for beamstop in- and out-position to both mach in (27 000). This way the beamstop will not be driven out when the hutch is opened, to avoid that the users forget to drive it in when restarting after entering the hutch.
30 -
31 -\\
32 -
33 -Prepare necessary controls for data collection:
34 -
35 -* ATK panels:
36 -** p11/simplon_filewriter/eh.01
37 -** p11/simplon_detector/eh.01
38 -*** count time = 0.0075
39 -*** trigger (**ints **if working without the chopper, # or triggers is 1, **exts** if with the chopper, # or triggers = number of images). Exts is also the standard trigger in normal crystallography. If GUI is used to take images (e.g. for beamstop alignment) the trigger mode will be forced by that and needs to be reverted manually for the users to continue.
40 -*** numer of images = 100 000
41 -*** number of images in container = 1000
42 -*** mode 16m/4M
43 -*** detector distance = 200 mm (usually)
44 -** p11/detectortower
45 -** p11/motor/eh.09
46 -* remote access to TapeDrive control laptop:
47 -** open terminal, execute command:          xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
48 - password: //written on control laptop
49 -//
50 -* Cameras:
51 -** haspp11ethcam1 → detector tower camera to monitor nozzle
52 -** haspp11ethcam4 →  goniometer camera to monitor tape from above
53 -* OnDa (on haspp11user04): 
54 -//This starts both GUIs (Frame Viewer & Crystallography GUI) and onda-monitor, the server component. The tool has a bunch of parameters which you can list with ./onda-runner.py —help.//\\
55 -** 16M mode →    cd /home/p11user/CfelSoft/202103_onda
56 - ./onda-runner.py onda-config/onda-config-Eiger16M.toml
57 -** 4M mode   →    cd /home/p11user/CfelSoft/202103_onda
58 - ./onda-runner.py onda-config/onda-config-Eiger4M.toml\\
59 -
60 -\\
61 -
62 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 Sample characteristics and preparation** ===
63 -
64 -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.
65 -
66 66  Preparation:
67 67  
68 -* 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
69 69  
70 70  [[image:attach:20211201_095534.jpg||height="250"]]
71 71  
72 72  \\
73 73  
74 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
75 -** ===
26 +----
76 76  
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
30 +
77 77  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!**
78 78  
79 79  Be aware to which channel and nozzle line your sample is connected.
... ... @@ -90,9 +90,11 @@
90 90  
91 91  \\
92 92  
93 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
94 -** ===
47 +----
95 95  
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 +** ==
51 +
96 96  The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
97 97  Now start the client. Same thing, a terminal will open, shortly after a small window.
98 98  
... ... @@ -99,9 +99,9 @@
99 99  Click 'Devices' in the **client session** to open the control window.
100 100  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
101 101  
102 -**Tape**
58 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
103 103  
104 -* Click on the 'main tape' icon
60 +* Click the 'main tape' icon
105 105  * Change the velocity by typing anything from **0.3-3.0 mm/s**
106 106  * Common velocity is 1.0-1.5 mm/s
107 107  * 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.
... ... @@ -110,7 +110,7 @@
110 110  
111 111  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
112 112  
113 -* Click an the 'nozzle' icon.
69 +* Click on the 'nozzle' icon.
114 114  * (((
115 115  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.
116 116  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
... ... @@ -119,6 +119,7 @@
119 119  (% 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);" %)** !!!**(%%)
120 120  \\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.
121 121  
78 +(% class="wrapped" %)
122 122  |=(((
123 123  \\
124 124  )))|=(((
... ... @@ -188,8 +188,10 @@
188 188  
189 189  \\
190 190  
191 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
148 +----
192 192  
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151 +
193 193  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).
194 194  
195 195  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -197,7 +197,7 @@
197 197  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
198 198  * Cut the first cm of the new tape roll, directly behind the black sticky part.
199 199  * 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.
200 -* 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!!!//
201 201  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
202 202  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
203 203  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -211,14 +211,17 @@
211 211  
212 212  \\
213 213  
214 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
173 +**
174 +**
215 215  {{/layout-cell}}
216 216  {{/layout-section}}
217 217  
218 218  {{layout-section ac:type="single"}}
219 219  {{layout-cell}}
220 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ===
180 +----
221 221  
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
183 +
222 222  start chopper gui from terminal:
223 223  
224 224  (% class="code" %)
... ... @@ -229,6 +229,7 @@
229 229  (% class="code" %)
230 230  (((
231 231   python chopperControl.py
194 +\\\\
232 232  )))
233 233  {{/layout-cell}}
234 234  {{/layout-section}}
... ... @@ -251,76 +251,72 @@
251 251  * (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
252 252  * (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps
253 253  ** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
254 -* (% 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 +//
255 255  {{/layout-cell}}
256 256  {{/layout-section}}
257 257  
258 258  {{layout-section ac:type="single"}}
259 259  {{layout-cell}}
260 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ===
224 +----
261 261  
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227 +
262 262  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
263 263  
264 264  (% class="code" %)
265 265  (((
266 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
232 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
267 267   password: written on control laptop (changes every 6 months)
268 268  )))
269 269  
270 - //>>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//
271 271  
272 272  \\
273 -
274 -Click "Start" icon in kamzik.
275 -
276 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
277 -
278 -----
279 279  {{/layout-cell}}
280 280  {{/layout-section}}
281 281  
282 -{{layout-section ac:type="two_equal"}}
242 +{{layout-section ac:type="two_left_sidebar"}}
283 283  {{layout-cell}}
284 284  **Check list:**
285 285  
286 286  (% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
287 287  
288 -* Open BS1  (//CrystalControl)//
289 -* Put collimator in (//CrystalControl)//
290 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
291 -* Open fast shutter (//CrystalControl)//
292 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
293 -* Close fast shutter (//CrystalControl)//
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
294 294  
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 +
295 295  \\
296 296  
297 -**Set run parameters and go 🏃💥**
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
298 298  
299 -1. Set your desired No. of frames
300 -1. Match exposure time with chopper setting
301 -1. Check trigger setting and match to chopper setting
302 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
303 -1. To start the run, click "<Call>" next to //exposure time//
304 -
305 305  \\
306 306  
307 -(% style="color: rgb(153,51,102);" %)**//Current bug~://**
263 +//**Set run parameters and go 🏃💥**//
308 308  
309 -(% 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}}
310 310  
311 -
312 -(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
313 -
314 -(% class="code" %)
315 -(((
316 - cd /gpfs/current/raw/scan_frames
317 - watch "ls -lrt <run number>/ | tail"
318 -\\\\\\\\
319 -)))
275 +{{layout-cell}}
276 +[[image:attach:Kamzik_run(2).PNG]]
320 320  {{/layout-cell}}
278 +{{/layout-section}}
321 321  
280 +{{layout-section ac:type="single"}}
322 322  {{layout-cell}}
323 -(% class="wrapped relative-table" style="width: 100.0%;" %)
282 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
324 324  |=(((
325 325  Parameter
326 326  )))|=(((
... ... @@ -331,7 +331,7 @@
331 331  |(((
332 332  Images number
333 333  )))|(((
334 -Set number of frames you want to collect
293 +number of frames you want to collect
335 335  )))|(% colspan="1" %)(((
336 336  usually 100k - 200k, but adjust according to hitrate
337 337  
... ... @@ -344,10 +344,7 @@
344 344  
345 345  \\
346 346  )))|(% colspan="1" %)(((
347 -chopper at 133 Hz → 3.7 ms
348 -
349 -chopper at 66 Hz   → 7.7 ms
350 -
306 +with chopper         → opening time displayed in chopper GUI
351 351  no chopper            → 7.7 ms
352 352  
353 353  ----
... ... @@ -367,29 +367,50 @@
367 367  \\
368 368  )))
369 369  |(% colspan="1" %)(((
370 -move_detector (distance)
326 +protein ID
371 371  )))|(% colspan="1" %)(((
372 -Set detector distance
328 +protein ID of crystal sample (see AMARCORD)
373 373  )))|(% colspan="1" %)(((
374 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
330 +\\
375 375  )))
376 -|(% colspan="1" %)(((
377 -Diode voltage
378 -)))|(% colspan="1" %)(((
379 -read out of diode
380 -)))|(% colspan="1" %)(((
381 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 
382 -Call local contact
383 -**
384 -)))
332 +
333 +----
385 385  {{/layout-cell}}
386 386  {{/layout-section}}
387 387  
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 +
388 388  {{layout-section ac:type="single"}}
389 389  {{layout-cell}}
390 390  ----
391 391  
392 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.9Troubleshooting"/}}14.9 Troubleshooting ===
369 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
393 393  
394 394  * (((
395 395  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
... ... @@ -417,6 +417,42 @@
417 417  * Sample empty?
418 418  * Nozzle or lines clogged? → flush with water, change nozzle
419 419  )))
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 +)))
420 420  {{/layout-cell}}
421 421  {{/layout-section}}
429 +
430 +{{layout-section ac:type="single"}}
431 +{{layout-cell}}
432 +\\
433 +{{/layout-cell}}
434 +{{/layout-section}}
422 422  {{/layout}}
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