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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 41.1
edited by ahenkel
on 2021-12-12 23:20
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 +
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 6  \\
7 7  
8 -{{toc minLevel="2"/}}
12 +\\
9 9  
10 10  \\
11 11  
12 -----
16 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1RevertfromCrystallographytoTapeDrive(P11staff/CFEL)"/}}**14.1 Revert from Crystallography to TapeDrive (P11 staff/CFEL)** ===
13 13  
14 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
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
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.
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.
17 17  
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 +
18 18  Preparation:
19 19  
20 -* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
72 +* 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 -----
78 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3ConnectingsampletoElveFlow,sampleexchange"/}}**14.3 Connecting sample to ElveFlow, sample exchange
79 +** ===
27 27  
28 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 -** ==
30 -
31 31  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!**
32 32  
33 33  Be aware to which channel and nozzle line your sample is connected.
... ... @@ -44,11 +44,9 @@
44 44  
45 45  \\
46 46  
47 -----
97 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4TapeDriveoperation"/}}**14.4 TapeDrive operation
98 +** ===
48 48  
49 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 -** ==
51 -
52 52  The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
53 53  Now start the client. Same thing, a terminal will open, shortly after a small window.
54 54  
... ... @@ -55,9 +55,9 @@
55 55  Click 'Devices' in the **client session** to open the control window.
56 56  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
57 57  
58 -==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
106 +**Tape**
59 59  
60 -* Click the 'main tape' icon
108 +* 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.
117 +* 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 -----
196 +=== {{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!!!//
205 +* 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.
... ... @@ -170,116 +170,74 @@
170 170  
171 171  \\
172 172  
173 -**
174 -**
175 -{{/layout-cell}}
176 -{{/layout-section}}
219 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Nozzleexchange"/}}**14.6 Nozzle exchange** ===
177 177  
178 -{{layout-section ac:type="single"}}
179 -{{layout-cell}}
180 -----
221 +\\
181 181  
182 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
223 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Datacollection"/}}**14.7 Data collection** ===
183 183  
184 -start chopper gui from terminal:
225 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
185 185  
186 186  (% class="code" %)
187 187  (((
188 - cd /gpfs/local/shared/ChopperControl
229 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
230 + password: written on control laptop (changes every 6 months)
189 189  )))
190 190  
191 -(% class="code" %)
192 -(((
193 - python chopperControl.py
194 -\\\\
195 -)))
196 -{{/layout-cell}}
197 -{{/layout-section}}
233 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
198 198  
199 -{{layout-section ac:type="two_equal"}}
200 -{{layout-cell}}
201 - [[image:attach:20211212_233140.jpg||height="250"]]
202 -{{/layout-cell}}
235 +\\
203 203  
204 -{{layout-cell}}
205 -**Chopper → no Chopper**
237 +Click "Start" icon in kamzik.
206 206  
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//
239 +[[image:attach:kamzik_run-tile.jpg||height="400"]]
211 211  
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 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}}
221 -
222 -{{layout-section ac:type="single"}}
223 -{{layout-cell}}
224 224  ----
225 -
226 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
227 -
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 -\\
239 239  {{/layout-cell}}
240 240  {{/layout-section}}
241 241  
242 -{{layout-section ac:type="two_left_sidebar"}}
245 +{{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.
251 +* Open BS1  (//CrystalControl)//
252 +* Put collimator in (//CrystalControl)//
253 +* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)//
254 +* Open fast shutter (//CrystalControl)//
255 +* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)//
256 +* 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 //
260 +**Set run parameters and go 🏃💥**
260 260  
262 +1. Set your desired No. of frames
263 +1. Match exposure time with chopper setting
264 +1. Check trigger setting and match to chopper setting
265 +1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it.
266 +1. To start the run, click "<Call>" next to //exposure time//
267 +
261 261  \\
262 262  
263 -//**Set run parameters and go 🏃💥**//
270 +(% 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}}
272 +(% 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]]
274 +
275 +(% style="color: rgb(0,0,0);" %)Check progress in terminal with:
276 +
277 +(% class="code" %)
278 +(((
279 + cd /gpfs/current/raw/scan_frames
280 + watch "ls -lrt <run number>/ | tail"
281 +\\\\\\\\
282 +)))
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%;" %)
286 +(% 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
297 +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
310 +chopper at 133 Hz → 3.7 ms
311 +
312 +chopper at 66 Hz   → 7.7 ms
313 +
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
333 +move_detector (distance)
327 327  )))|(% colspan="1" %)(((
328 -protein ID of crystal sample (see AMARCORD)
335 +Set detector distance
329 329  )))|(% colspan="1" %)(((
330 -\\
337 +200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
331 331  )))
332 -
333 -----
339 +|(% colspan="1" %)(((
340 +Diode voltage
341 +)))|(% colspan="1" %)(((
342 +read out of diode
343 +)))|(% colspan="1" %)(((
344 +**~~ 0 !!! higher values indicate missaligned beam stop!!! 
345 +Call local contact
346 +**
347 +)))
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** ==
355 +=== {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Troubleshooting"/}}14.8 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}}
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