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Last modified by chatzies on 2025-11-27 11:35
From version 36.1
edited by ahenkel
on 2021-12-12 22:53
Change comment: There is no comment for this version
To version 49.1
edited by ahenkel
on 2022-04-04 14:43
Change comment: There is no comment for this version

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1 +{{layout}}
2 +{{layout-section ac:type="single"}}
3 +{{layout-cell}}
4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="250"]]
1 1  
2 -
3 -{{toc/}}
4 -
5 -[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
6 -
7 7  \\
8 8  
9 -\\
8 +{{toc minLevel="2"/}}
10 10  
11 11  \\
12 12  
13 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
12 +----
14 14  
15 -* remove vortex
16 -* beamstop to out-position?
17 -* remove goniometer. The airbearing should be stopped (p11/servermotor/eh.1.01)
18 -* 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.
19 -* stop refill of the robot dewar and empty the dewar, warm up.
20 -* Disable backlight (unplug Festo connection). (% style="color: rgb(255,0,0);" %)//Is this still needed?//
21 -* (% 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.
22 -* (% 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** ==
23 23  
24 -(% 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.
25 -
26 -\\
27 -
28 -* 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).//
29 -* (% 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.
30 -* (% 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.
31 -
32 -\\
33 -
34 -Prepare necessary controls for data collection:
35 -
36 -* ATK panels:
37 -** p11/simplon_filewriter/eh.01
38 -** p11/simplon_detector/eh.01
39 -*** count time = 0.0075
40 -*** 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.
41 -*** numer of images = 100 000
42 -*** number of images in container = 1000
43 -*** mode 16m/4M
44 -*** detector distance = 200 mm (usually)
45 -** p11/detectortower
46 -** p11/motor/eh.09
47 -* remote access to TapeDrive control laptop:
48 -** open terminal, execute command:          xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
49 - password: //written on control laptop
50 -//
51 -* Cameras:
52 -** haspp11ethcam1 → detector tower camera to monitor nozzle
53 -** haspp11ethcam4 →  goniometer camera to monitor tape from above
54 -* OnDa (on haspp11user04): 
55 -//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.//\\
56 -** 16M mode →    cd /home/p11user/CfelSoft/202103_onda
57 - ./onda-runner.py onda-config/onda-config-Eiger16M.toml
58 -** 4M mode   →    cd /home/p11user/CfelSoft/202103_onda
59 - ./onda-runner.py onda-config/onda-config-Eiger4M.toml\\
60 -
61 -\\
62 -
63 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2Samplecharacteristicsandpreparation"/}}**14.2 Sample characteristics and preparation** ===
64 -
65 65  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.
66 66  
67 67  Preparation:
... ... @@ -72,9 +72,11 @@
72 72  
73 73  \\
74 74  
75 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
76 -** ===
26 +----
77 77  
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
30 +
78 78  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!**
79 79  
80 80  Be aware to which channel and nozzle line your sample is connected.
... ... @@ -91,9 +91,11 @@
91 91  
92 92  \\
93 93  
94 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
95 -** ===
47 +----
96 96  
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 +** ==
51 +
97 97  The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
98 98  Now start the client. Same thing, a terminal will open, shortly after a small window.
99 99  
... ... @@ -100,7 +100,7 @@
100 100  Click 'Devices' in the **client session** to open the control window.
101 101  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
102 102  
103 -**Tape**
58 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
104 104  
105 105  * Click on the 'main tape' icon
106 106  * Change the velocity by typing anything from **0.3-3.0 mm/s**
... ... @@ -190,8 +190,10 @@
190 190  
191 191  \\
192 192  
193 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ===
148 +----
194 194  
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
151 +
195 195  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).
196 196  
197 197  * Remove the (almost) empty feeder roll by pulling it upwards.
... ... @@ -213,23 +213,86 @@
213 213  
214 214  \\
215 215  
216 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
173 +**
174 +**
175 +{{/layout-cell}}
176 +{{/layout-section}}
217 217  
218 -\\
178 +{{layout-section ac:type="single"}}
179 +{{layout-cell}}
180 +----
219 219  
220 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Datacollection"/}}**14.7 Data collection** ===
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
221 221  
184 +start chopper gui from terminal:
185 +
186 +(% class="code" %)
187 +(((
188 + cd /gpfs/local/shared/ChopperControl
189 +)))
190 +
191 +(% class="code" %)
192 +(((
193 + python chopperControl.py
194 +\\\\
195 +)))
196 +{{/layout-cell}}
197 +{{/layout-section}}
198 +
199 +{{layout-section ac:type="two_equal"}}
200 +{{layout-cell}}
201 + [[image:attach:20211212_233140.jpg||height="250"]]
202 +{{/layout-cell}}
203 +
204 +{{layout-cell}}
205 +**Chopper → no Chopper**
206 +
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//
211 +
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
213 +
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//
218 +{{/layout-cell}}
219 +{{/layout-section}}
220 +
221 +{{layout-section ac:type="single"}}
222 +{{layout-cell}}
223 +----
224 +
225 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
226 +
222 222  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
223 223  
224 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
225 - password: //written on control laptop (changes every 6 months)//
229 +(% class="code" %)
230 +(((
231 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
232 + password: written on control laptop (changes every 6 months)
233 +)))
226 226  
227 227   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
228 228  
229 229  \\
230 230  
239 +Click "Start" icon in kamzik.
240 +
241 +[[image:attach:kamzik_run-tile.jpg||height="400"]]
242 +
243 +----
244 +{{/layout-cell}}
245 +{{/layout-section}}
246 +
247 +{{layout-section ac:type="two_equal"}}
248 +{{layout-cell}}
231 231  **Check list:**
232 232  
251 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
252 +
233 233  * Open BS1  (//CrystalControl)//
234 234  * Put collimator in (//CrystalControl)//
235 235  * Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
... ... @@ -239,13 +239,33 @@
239 239  
240 240  \\
241 241  
242 -**Start run in kamzik
243 -**
262 +**Set run parameters and go 🏃💥**
244 244  
245 -Click "Start" icon in kamzik.
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//
246 246  
247 -[[image:attach:kamzik_run-tile.jpg||height="400"]]
270 +\\
248 248  
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 +)))
285 +{{/layout-cell}}
286 +
287 +{{layout-cell}}
288 +(% class="wrapped relative-table" style="width: 100.0%;" %)
249 249  |=(((
250 250  Parameter
251 251  )))|=(((
... ... @@ -303,52 +303,55 @@
303 303  )))|(% colspan="1" %)(((
304 304  read out of diode
305 305  )))|(% colspan="1" %)(((
306 -**~~ 0 !!! higher values indicate missaligned beam stop!!!**
346 +**~~ 0 !!! higher values indicate missaligned beam stop!!! 
347 +Call local contact
348 +**
307 307  )))
350 +{{/layout-cell}}
351 +{{/layout-section}}
308 308  
353 +{{layout-section ac:type="single"}}
354 +{{layout-cell}}
309 309  ----
310 310  
311 -(% class="task-list" %)
312 -(((
313 -{{task reference="/Tasks/Task_6" status="InProgress"}}
314 -Set your desired No. of frames
315 -{{/task}}
357 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
316 316  
317 -{{task reference="/Tasks/Task_7" status="InProgress"}}
318 -Match exposure time with chopper setting
319 -{{/task}}
359 +* (((
360 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
320 320  
321 -{{task reference="/Tasks/Task_8" status="InProgress"}}
322 -Check trigger setting and match to chopper setting
323 -{{/task}}
324 -
325 -{{task reference="/Tasks/Task_9" status="InProgress"}}
326 -Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
327 -{{/task}}
328 -
329 -{{task reference="/Tasks/Task_10" status="InProgress"}}
330 -To start the run, click "<Call>" next to //exposure time//
331 -{{/task}}
362 +* Tape roll empty?
363 +* motor connected (icon green)?
332 332  )))
333 333  
334 -----
335 -
336 336  \\
337 337  
338 -\\
339 -
340 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Troubleshooting"/}}14.8 Troubleshooting ===
341 -
342 342  * (((
343 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
344 -)))
345 -* (((
346 346  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
370 +
371 +* displayed in green=connected?
372 +* nozzle holder colliding somewhere?
373 +* motor limits reached? → position displayed in red
347 347  )))
375 +
376 +\\
377 +
348 348  * (((
349 349  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
380 +
381 +* channel turned on?
382 +* Sample empty?
383 +* Nozzle or lines clogged? → flush with water, change nozzle
350 350  )))
385 +* (((
386 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
351 351  
352 -\\
353 -
354 -\\
388 +* First, restart kamzik (server+client) and see if this solves the issue
389 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
390 +* If nothing works, kill the Simplon process and then start the server again:
391 +** ssh haspp11exp03
392 +** ps -ef | grep Simplon
393 +** kill -9 simplon_process_id
394 +)))
395 +{{/layout-cell}}
396 +{{/layout-section}}
397 +{{/layout}}
Confluence.Code.ConfluencePageClass[0]
Id
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1 -236824562
1 +250178591
URL
... ... @@ -1,1 +1,1 @@
1 -https://confluence.desy.de/spaces/11/pages/236824562/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/250178591/14. Serial Crystallography: CFEL TapeDrive