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Last modified by chatzies on 2025-11-27 11:35
From version 38.1
edited by ahenkel
on 2021-12-12 22:59
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

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1 1  {{layout}}
2 2  {{layout-section ac:type="single"}}
3 3  {{layout-cell}}
4 -
5 -
6 -{{toc/}}
7 -
8 8  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
9 9  
10 10  \\
11 11  
12 -\\
8 +{{toc minLevel="2"/}}
13 13  
14 14  \\
15 15  
16 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
12 +----
17 17  
18 -* remove vortex
19 -* beamstop to out-position?
20 -* remove goniometer. The airbearing should be stopped (p11/servermotor/eh.1.01)
21 -* 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.
22 -* stop refill of the robot dewar and empty the dewar, warm up.
23 -* Disable backlight (unplug Festo connection). (% style="color: rgb(255,0,0);" %)//Is this still needed?//
24 -* (% 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.
25 -* (% 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** ==
26 26  
27 -(% 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.
28 28  
29 -\\
30 -
31 -* 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).//
32 -* (% 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.
33 -* (% 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.
34 -
35 -\\
36 -
37 -Prepare necessary controls for data collection:
38 -
39 -* ATK panels:
40 -** p11/simplon_filewriter/eh.01
41 -** p11/simplon_detector/eh.01
42 -*** count time = 0.0075
43 -*** 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.
44 -*** numer of images = 100 000
45 -*** number of images in container = 1000
46 -*** mode 16m/4M
47 -*** detector distance = 200 mm (usually)
48 -** p11/detectortower
49 -** p11/motor/eh.09
50 -* remote access to TapeDrive control laptop:
51 -** open terminal, execute command:          xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
52 - password: //written on control laptop
53 -//
54 -* Cameras:
55 -** haspp11ethcam1 → detector tower camera to monitor nozzle
56 -** haspp11ethcam4 →  goniometer camera to monitor tape from above
57 -* OnDa (on haspp11user04): 
58 -//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.//\\
59 -** 16M mode →    cd /home/p11user/CfelSoft/202103_onda
60 - ./onda-runner.py onda-config/onda-config-Eiger16M.toml
61 -** 4M mode   →    cd /home/p11user/CfelSoft/202103_onda
62 - ./onda-runner.py onda-config/onda-config-Eiger4M.toml\\
63 -
64 -\\
65 -
66 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 Sample characteristics and preparation** ===
67 -
68 -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.
69 -
70 70  Preparation:
71 71  
72 -* 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
73 73  
74 74  [[image:attach:20211201_095534.jpg||height="250"]]
75 75  
76 76  \\
77 77  
78 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
79 -** ===
26 +----
80 80  
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
30 +
81 81  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!**
82 82  
83 83  Be aware to which channel and nozzle line your sample is connected.
... ... @@ -94,9 +94,11 @@
94 94  
95 95  \\
96 96  
97 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
98 -** ===
47 +----
99 99  
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 +** ==
51 +
100 100  The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
101 101  Now start the client. Same thing, a terminal will open, shortly after a small window.
102 102  
... ... @@ -103,9 +103,9 @@
103 103  Click 'Devices' in the **client session** to open the control window.
104 104  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
105 105  
106 -**Tape**
58 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
107 107  
108 -* Click on the 'main tape' icon
60 +* Click the 'main tape' icon
109 109  * Change the velocity by typing anything from **0.3-3.0 mm/s**
110 110  * Common velocity is 1.0-1.5 mm/s
111 111  * 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.
... ... @@ -114,7 +114,7 @@
114 114  
115 115  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
116 116  
117 -* Click an the 'nozzle' icon.
69 +* Click on the 'nozzle' icon.
118 118  * (((
119 119  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.
120 120  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
... ... @@ -193,8 +193,10 @@
193 193  
194 194  \\
195 195  
196 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
148 +----
197 197  
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151 +
198 198  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).
199 199  
200 200  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -202,7 +202,7 @@
202 202  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
203 203  * Cut the first cm of the new tape roll, directly behind the black sticky part.
204 204  * 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.
205 -* 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!!!//
206 206  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
207 207  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
208 208  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -216,78 +216,116 @@
216 216  
217 217  \\
218 218  
219 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
173 +**
174 +**
175 +{{/layout-cell}}
176 +{{/layout-section}}
220 220  
221 -\\
178 +{{layout-section ac:type="single"}}
179 +{{layout-cell}}
180 +----
222 222  
223 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Datacollection"/}}**14.7 Data collection** ===
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
224 224  
225 -Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
184 +start chopper gui from terminal:
226 226  
227 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
228 - password: //written on control laptop (changes every 6 months)//
186 +(% class="code" %)
187 +(((
188 + cd /gpfs/local/shared/ChopperControl
189 +)))
229 229  
230 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
191 +(% class="code" %)
192 +(((
193 + python chopperControl.py
194 +\\\\
195 +)))
196 +{{/layout-cell}}
197 +{{/layout-section}}
231 231  
232 -\\
199 +{{layout-section ac:type="two_equal"}}
200 +{{layout-cell}}
201 + [[image:attach:20211212_233140.jpg||height="250"]]
202 +{{/layout-cell}}
233 233  
234 -**Check list:**
204 +{{layout-cell}}
205 +**Chopper → no Chopper**
235 235  
236 -* Open BS1  (//CrystalControl)//
237 -* Put collimator in (//CrystalControl)//
238 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
239 -* Open fast shutter (//CrystalControl)//
240 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
241 -* Close fast shutter (//CrystalControl)//
207 +* decrease frequency by max. 10 Hz steps\\
208 +** click arrow down 10x, "Set", arrow down 10x, "Set", ....
209 +* at frequency = 10 Hz, click "Stop"
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
242 242  
243 -\\
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
244 244  
245 -**Start run in kamzik
246 -**
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 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 +//
219 +{{/layout-cell}}
220 +{{/layout-section}}
247 247  
248 -Click "Start" icon in kamzik.
222 +{{layout-section ac:type="single"}}
223 +{{layout-cell}}
224 +----
249 249  
250 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
251 251  
252 -----
228 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
229 +
230 +(% class="code" %)
231 +(((
232 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
233 + password: written on control laptop (changes every 6 months)
234 +)))
235 +
236 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
237 +
238 +\\
253 253  {{/layout-cell}}
254 254  {{/layout-section}}
255 255  
256 -{{layout-section ac:type="two_equal"}}
242 +{{layout-section ac:type="two_left_sidebar"}}
257 257  {{layout-cell}}
244 +**Check list:**
245 +
246 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
247 +
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
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 +
258 258  \\
259 259  
260 -(% class="task-list" %)
261 -(((
262 -{{task reference="/Tasks/Task_16" status="InProgress"}}
263 -(% class="task-list" %)
264 -(((
265 -{{task reference="/Tasks/Task_22" status="InProgress"}}
266 -Set your desired No. of frames
267 -{{/task}}
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
268 268  
269 -{{task reference="/Tasks/Task_17" status="InProgress"}}
270 -Match exposure time with chopper setting
271 -{{/task}}
261 +\\
272 272  
273 -{{task reference="/Tasks/Task_18" status="InProgress"}}
274 -Check trigger setting and match to chopper setting
275 -{{/task}}
263 +//**Set run parameters and go 🏃💥**//
276 276  
277 -{{task reference="/Tasks/Task_19" status="InProgress"}}
278 -Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
279 -{{/task}}
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}}
280 280  
281 -{{task reference="/Tasks/Task_20" status="InProgress"}}
282 -To start the run, click "<Call>" next to //exposure time//
283 -{{/task}}
284 -)))
285 -{{/task}}
286 -)))
275 +{{layout-cell}}
276 +[[image:attach:Kamzik_run(2).PNG]]
287 287  {{/layout-cell}}
278 +{{/layout-section}}
288 288  
280 +{{layout-section ac:type="single"}}
289 289  {{layout-cell}}
290 -(% class="wrapped" %)
282 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
291 291  |=(((
292 292  Parameter
293 293  )))|=(((
... ... @@ -298,7 +298,7 @@
298 298  |(((
299 299  Images number
300 300  )))|(((
301 -Set number of frames you want to collect
293 +number of frames you want to collect
302 302  )))|(% colspan="1" %)(((
303 303  usually 100k - 200k, but adjust according to hitrate
304 304  
... ... @@ -311,10 +311,7 @@
311 311  
312 312  \\
313 313  )))|(% colspan="1" %)(((
314 -chopper at 133 Hz → 3.7 ms
315 -
316 -chopper at 66 Hz   → 7.7 ms
317 -
306 +with chopper         → opening time displayed in chopper GUI
318 318  no chopper            → 7.7 ms
319 319  
320 320  ----
... ... @@ -334,35 +334,113 @@
334 334  \\
335 335  )))
336 336  |(% colspan="1" %)(((
337 -move_detector (distance)
326 +protein ID
338 338  )))|(% colspan="1" %)(((
339 -Set detector distance
328 +protein ID of crystal sample (see AMARCORD)
340 340  )))|(% colspan="1" %)(((
341 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
330 +\\
342 342  )))
343 -|(% colspan="1" %)(((
344 -Diode voltage
345 -)))|(% colspan="1" %)(((
346 -read out of diode
347 -)))|(% colspan="1" %)(((
348 -**~~ 0 !!! higher values indicate missaligned beam stop!!!**
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 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Troubleshooting"/}}14.8 Troubleshooting ===
367 +----
356 356  
369 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
370 +
357 357  * (((
358 358  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
373 +
374 +* Tape roll empty?
375 +* motor connected (icon green)?
359 359  )))
377 +
378 +\\
379 +
360 360  * (((
361 361  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
382 +
383 +* displayed in green=connected?
384 +* nozzle holder colliding somewhere?
385 +* motor limits reached? → position displayed in red
362 362  )))
387 +
388 +\\
389 +
363 363  * (((
364 364  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
392 +
393 +* channel turned on?
394 +* Sample empty?
395 +* Nozzle or lines clogged? → flush with water, change nozzle
365 365  )))
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 +)))
366 366  {{/layout-cell}}
367 367  {{/layout-section}}
429 +
430 +{{layout-section ac:type="single"}}
431 +{{layout-cell}}
432 +\\
433 +{{/layout-cell}}
434 +{{/layout-section}}
368 368  {{/layout}}
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