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Last modified by chatzies on 2025-11-27 11:35
From version 68.1
edited by ahenkel
on 2022-05-07 18:53
Change comment: There is no comment for this version
To version 77.1
edited by tabermah
on 2024-12-03 11:26
Change comment: There is no comment for this version

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Title
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1 -14. Serial Crystallography: CFEL TapeDrive
1 +10. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.ahenkel
1 +XWiki.tabermah
Content
... ... @@ -3,11 +3,9 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 -\\
7 7  
8 8  {{toc minLevel="2"/}}
9 9  
10 -\\
11 11  
12 12  ----
13 13  
... ... @@ -21,11 +21,12 @@
21 21  
22 22  [[image:attach:20211201_095534.jpg||height="250"]]
23 23  
24 -\\
25 25  
26 26  ----
27 27  
28 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
25 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26 +
27 +*
29 29  ** ==
30 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!**
... ... @@ -42,14 +42,15 @@
42 42  
43 43  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
44 44  
45 -\\
46 46  
47 47  ----
48 48  
49 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
47 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48 +
49 +*
50 50  ** ==
51 51  
52 -The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
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 55  Click 'Devices' in the **client session** to open the control window.
... ... @@ -61,7 +61,7 @@
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.
64 -\\
64 +
65 65  * [[image:attach:kamzik_tape.PNG||height="400"]]
66 66  
67 67  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
... ... @@ -72,16 +72,16 @@
72 72  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
73 73  
74 74  
75 -(% 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);" %)** !!!**(%%)
75 +(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
76 76  \\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.
77 77  
78 78  (% class="wrapped" %)
79 79  |=(((
80 -\\
80 +
81 81  )))|=(((
82 82  direction
83 83  )))|=(((
84 -recommended step size
84 +recommended step size
85 85  for visual adjustment
86 86  )))|=(% colspan="1" %)(((
87 87  recommended step size
... ... @@ -116,8 +116,8 @@
116 116  be careful with -z, tape could be pushed out of focus
117 117  )))
118 118  
119 -**
120 -\\**
119 +
120 +
121 121  )))
122 122  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
123 123  
... ... @@ -125,25 +125,19 @@
125 125  
126 126  * The chiller circulates fluid through the gas nozzle.
127 127  
128 -\\
129 129  
130 130  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
131 131  
132 -\\
133 133  
134 134  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
135 135  
136 -\\
137 137  
138 138  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
139 139  
140 140   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
141 - password: //written on control laptop (changes every 6 months)
142 -//
138 + password: //written on control laptop (changes every 6 months)//
143 143  
144 -\\
145 145  
146 -\\
147 147  
148 148  ----
149 149  
... ... @@ -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!!!//
153 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!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.
... ... @@ -163,15 +163,11 @@
163 163  * Close tape stabilizer.
164 164  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
165 165  
166 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 -**
160 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
168 168  
169 -\\
170 170  
171 -\\
172 172  
173 -**
174 -**
164 +
175 175  {{/layout-cell}}
176 176  {{/layout-section}}
177 177  
... ... @@ -185,13 +185,13 @@
185 185  
186 186  (% class="code" %)
187 187  (((
188 - cd /gpfs/local/shared/ChopperControl
178 + cd /gpfs/local/shared/ChopperControl          
189 189  )))
190 190  
191 191  (% class="code" %)
192 192  (((
193 193   python chopperControl.py
194 -\\\\
184 +\\
195 195  )))
196 196  {{/layout-cell}}
197 197  {{/layout-section}}
... ... @@ -204,23 +204,24 @@
204 204  {{layout-cell}}
205 205  **Chopper → no Chopper**
206 206  
207 -* decrease frequency by max. 10 Hz steps\\
197 +* decrease frequency by max. 10 Hz steps
208 208  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
209 209  * at frequency = 10 Hz, click "Stop"
210 -* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
200 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
211 211  
212 -(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
202 +(% style="color:#000000" %)**no Chopper → Chopper**
213 213  
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 (technical exposure will always be 7.7 ms, since max. frame rate is 133 Hz
218 -//
204 +* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
205 +* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
206 +** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
207 +* (% style="color:#000000" %)//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//
219 219  {{/layout-cell}}
220 220  {{/layout-section}}
221 221  
222 222  {{layout-section ac:type="single"}}
223 223  {{layout-cell}}
213 +----
214 +
224 224  == {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
225 225  
226 226  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
... ... @@ -227,13 +227,13 @@
227 227  
228 228  (% class="code" %)
229 229  (((
230 - xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
221 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
231 231   password: written on control laptop (changes every 6 months)
232 232  )))
233 233  
234 234   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
235 235  
236 -\\
227 +
237 237  {{/layout-cell}}
238 238  {{/layout-section}}
239 239  
... ... @@ -241,37 +241,39 @@
241 241  {{layout-cell}}
242 242  **Check list:**
243 243  
244 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
235 +(% style="color:#ff0000" %)//always after entering the hutch!//
245 245  
246 -(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
237 +(% style="color:#000000" %)Click "Run" icon in kamzik.
247 247  
248 -* Put collimator in
249 -** Put detector distance 200 in //prepare_for_measurement (      )
250 -//
251 -** Click "<Call>" next to //prepare_for_measurement//
239 +* Put detector distance 200 in //prepare_for_measurement (      )//
240 +* Click "<Call>" next to //prepare_for_measurement//
241 +This will:
242 +** drive the collimator in //IN// position
243 +** drive detector to 200 mm
252 252  
253 -\\
254 254  
255 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
246 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
256 256  
257 -\\
258 258  
259 259  //**Set run parameters and go 🏃💥**//
260 260  
261 261  1. Set your desired No. of frames
252 +1. Enter the protein ID of your crystal sample
262 262  1. Match exposure time with chopper setting or set desired exposure time
263 263  1. Check trigger setting and match to chopper setting
255 +no chopper → external triffer //off//
256 + chopper → external trigger// on//
264 264  1. To start the run, click "<Call>" next to //start_run (exposure    )//
265 265  {{/layout-cell}}
266 266  
267 267  {{layout-cell}}
268 -[[image:attach:Kamzik_run(2).PNG||height="400"]]
261 +[[image:attach:Kamzik_run(2).PNG]]
269 269  {{/layout-cell}}
270 270  {{/layout-section}}
271 271  
272 -{{layout-section ac:type="two_equal"}}
265 +{{layout-section ac:type="single"}}
273 273  {{layout-cell}}
274 -(% class="relative-table" %)
267 +(% class="relative-table wrapped" style="width:55.9569%" %)
275 275  |=(((
276 276  Parameter
277 277  )))|=(((
... ... @@ -282,7 +282,7 @@
282 282  |(((
283 283  Images number
284 284  )))|(((
285 -Set number of frames you want to collect
278 +number of frames you want to collect
286 286  )))|(% colspan="1" %)(((
287 287  usually 100k - 200k, but adjust according to hitrate
288 288  
... ... @@ -293,12 +293,9 @@
293 293  )))|(((
294 294  exposure time of Eiger
295 295  
296 -\\
289 +
297 297  )))|(% colspan="1" %)(((
298 -chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
299 -
300 -chopper at 66 Hz   → 7.7 ms
301 -
291 +with chopper         → opening time displayed in chopper GUI
302 302  no chopper            → 7.7 ms
303 303  
304 304  ----
... ... @@ -308,7 +308,7 @@
308 308  )))|(((
309 309  changes automatically
310 310  )))|(% colspan="1" %)(((
311 -\\
301 +
312 312  )))
313 313  |(% colspan="1" %)(((
314 314  Detector distance
... ... @@ -315,17 +315,21 @@
315 315  )))|(% colspan="1" %)(((
316 316  current detector postion readout
317 317  )))|(% colspan="1" %)(((
318 -\\
308 +
319 319  )))
320 320  |(% colspan="1" %)(((
321 -move_detector (distance)
311 +protein ID
322 322  )))|(% colspan="1" %)(((
323 -Set detector distance
313 +protein ID of crystal sample (see AMARCORD)
324 324  )))|(% colspan="1" %)(((
325 -200.0 mm   (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"
315 +
326 326  )))
317 +
318 +----
327 327  {{/layout-cell}}
320 +{{/layout-section}}
328 328  
322 +{{layout-section ac:type="two_equal"}}
329 329  {{layout-cell}}
330 330  **After data collection/Before entering the exp. hutch:**
331 331  
... ... @@ -335,8 +335,18 @@
335 335  11. Drive the detector back to 1500 mm
336 336  1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
337 337  
338 -[[image:attach:Screenshot from 2022-04-04 19-36-29.png||height="400"]]
332 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
339 339  {{/layout-cell}}
334 +
335 +{{layout-cell}}
336 +
337 +
338 +
339 +
340 +
341 +
342 +[[image:attach:safety_kamzik.PNG]]
343 +{{/layout-cell}}
340 340  {{/layout-section}}
341 341  
342 342  {{layout-section ac:type="single"}}
... ... @@ -352,7 +352,6 @@
352 352  * motor connected (icon green)?
353 353  )))
354 354  
355 -\\
356 356  
357 357  * (((
358 358  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
... ... @@ -362,7 +362,6 @@
362 362  * motor limits reached? → position displayed in red
363 363  )))
364 364  
365 -\\
366 366  
367 367  * (((
368 368  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
... ... @@ -372,7 +372,6 @@
372 372  * Nozzle or lines clogged? → flush with water, change nozzle
373 373  )))
374 374  
375 -\\
376 376  
377 377  * (((
378 378  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
... ... @@ -380,12 +380,15 @@
380 380  * First, restart kamzik (server+client) and see if this solves the issue
381 381  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
382 382  * (((
383 -If nothing works, kill the Simplon process and then start the server again:* (((
384 +If nothing works, kill the Simplon process and then start the server again:*
385 +
386 +(((
384 384  (% class="code" %)
385 385  (((
386 386  ssh haspp11exp03
387 387  )))
388 388  )))
392 +
389 389  * (((
390 390  (% class="code" %)
391 391  (((
... ... @@ -399,6 +399,7 @@
399 399  )))
400 400  )))
401 401  )))
406 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
402 402  )))
403 403  {{/layout-cell}}
404 404  {{/layout-section}}
... ... @@ -405,7 +405,7 @@
405 405  
406 406  {{layout-section ac:type="single"}}
407 407  {{layout-cell}}
408 -\\
413 +
409 409  {{/layout-cell}}
410 410  {{/layout-section}}
411 411  {{/layout}}
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1 -254729370
1 +235031805
URL
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1 -https://confluence.desy.de/spaces/11/pages/254729370/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive