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Last modified by chatzies on 2025-11-27 11:35
From version 78.1
edited by tabermah
on 2024-12-03 11:34
Change comment: There is no comment for this version
To version 75.1
edited by ahenkel
on 2022-05-07 20:15
Change comment: There is no comment for this version

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Title
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1 -08. Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
Author
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1 -XWiki.tabermah
1 +XWiki.ahenkel
Content
... ... @@ -3,9 +3,11 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 7  {{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 11  
... ... @@ -19,12 +19,11 @@
19 19  
20 20  [[image:attach:20211201_095534.jpg||height="250"]]
21 21  
24 +\\
22 22  
23 23  ----
24 24  
25 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** ==
26 -
27 -*
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
28 28  ** ==
29 29  
30 30  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!**
... ... @@ -41,15 +41,14 @@
41 41  
42 42  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
43 43  
45 +\\
44 44  
45 45  ----
46 46  
47 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** ==
48 -
49 -*
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
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:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
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);" %)** !!!**(%%)
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
... ... @@ -116,7 +116,8 @@
116 116  be careful with -z, tape could be pushed out of focus
117 117  )))
118 118  
119 -
119 +**
120 +\\**
120 120  )))
121 121  * [[image:attach:kamzik_nozzle.PNG||height="400"]]
122 122  
... ... @@ -124,18 +124,25 @@
124 124  
125 125  * The chiller circulates fluid through the gas nozzle.
126 126  
128 +\\
129 +
127 127  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
128 128  
132 +\\
129 129  
130 130  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
131 131  
136 +\\
132 132  
133 133  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
134 134  
135 135   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
136 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
137 137  
144 +\\
138 138  
146 +\\
139 139  
140 140  ----
141 141  
... ... @@ -148,7 +148,7 @@
148 148  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
149 149  * Cut the first cm of the new tape roll, directly behind the black sticky part.
150 150  * 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.
151 -* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
159 +* Open magnetic tape stabilizer on the **left side**. (% style="color: rgb(255,0,0);" %)//!!!BEAMSTOP!!!//
152 152  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
153 153  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
154 154  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -155,11 +155,15 @@
155 155  * Close tape stabilizer.
156 156  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
157 157  
158 -**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
166 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]
167 +**
159 159  
169 +\\
160 160  
171 +\\
161 161  
162 -
173 +**
174 +**
163 163  {{/layout-cell}}
164 164  {{/layout-section}}
165 165  
... ... @@ -173,13 +173,13 @@
173 173  
174 174  (% class="code" %)
175 175  (((
176 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
177 177  )))
178 178  
179 179  (% class="code" %)
180 180  (((
181 181   python chopperControl.py
182 -\\
194 +\\\\
183 183  )))
184 184  {{/layout-cell}}
185 185  {{/layout-section}}
... ... @@ -192,17 +192,18 @@
192 192  {{layout-cell}}
193 193  **Chopper → no Chopper**
194 194  
195 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
196 196  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
197 197  * at frequency = 10 Hz, click "Stop"
198 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
199 199  
200 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
201 201  
202 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
203 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
204 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
205 -* (% 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//
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 +//
206 206  {{/layout-cell}}
207 207  {{/layout-section}}
208 208  
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216 216  
217 217  (% class="code" %)
218 218  (((
219 - xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
232 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
220 220   password: written on control laptop (changes every 6 months)
221 221  )))
222 222  
223 223   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
224 224  
225 -
238 +\\
226 226  {{/layout-cell}}
227 227  {{/layout-section}}
228 228  
... ... @@ -230,26 +230,31 @@
230 230  {{layout-cell}}
231 231  **Check list:**
232 232  
233 -(% style="color:#ff0000" %)//always after entering the hutch!//
246 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
234 234  
235 -(% style="color:#000000" %)Click "Run" icon in kamzik.
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
236 236  
237 -* Put detector distance 200 in //prepare_for_measurement (      )//
238 -* Click "<Call>" next to //prepare_for_measurement//
239 -This will:
250 +* Put detector distance 200 in //prepare_for_measurement (      )
251 +//
252 +* Click "<Call>" next to //prepare_for_measurement
253 +//This will:\\
240 240  ** drive the collimator in //IN// position
241 241  ** drive detector to 200 mm
242 242  
243 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
257 +\\
244 244  
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
260 +
261 +\\
262 +
245 245  //**Set run parameters and go 🏃💥**//
246 246  
247 247  1. Set your desired No. of frames
248 -1. Enter the protein ID of your crystal sample
249 249  1. Match exposure time with chopper setting or set desired exposure time
250 250  1. Check trigger setting and match to chopper setting
251 -no chopper → external triffer //off//
252 - chopper → external trigger// on//
268 +no chopper → external triffer //off
269 +// chopper → external trigger// on
270 +//
253 253  1. To start the run, click "<Call>" next to //start_run (exposure    )//
254 254  {{/layout-cell}}
255 255  
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260 260  
261 261  {{layout-section ac:type="single"}}
262 262  {{layout-cell}}
263 -(% class="relative-table wrapped" style="width:55.9569%" %)
281 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
264 264  |=(((
265 265  Parameter
266 266  )))|=(((
... ... @@ -282,9 +282,12 @@
282 282  )))|(((
283 283  exposure time of Eiger
284 284  
285 -
303 +\\
286 286  )))|(% colspan="1" %)(((
287 -with chopper         → opening time displayed in chopper GUI
305 +chopper at 133 Hz → 7.7 ms (opening time will be 3.7)
306 +
307 +chopper at 66 Hz   → 7.7 ms
308 +
288 288  no chopper            → 7.7 ms
289 289  
290 290  ----
... ... @@ -294,7 +294,7 @@
294 294  )))|(((
295 295  changes automatically
296 296  )))|(% colspan="1" %)(((
297 -
318 +\\
298 298  )))
299 299  |(% colspan="1" %)(((
300 300  Detector distance
... ... @@ -301,15 +301,8 @@
301 301  )))|(% colspan="1" %)(((
302 302  current detector postion readout
303 303  )))|(% colspan="1" %)(((
304 -
325 +\\
305 305  )))
306 -|(% colspan="1" %)(((
307 -protein ID
308 -)))|(% colspan="1" %)(((
309 -protein ID of crystal sample (see AMARCORD)
310 -)))|(% colspan="1" %)(((
311 -
312 -)))
313 313  
314 314  ----
315 315  {{/layout-cell}}
... ... @@ -329,11 +329,15 @@
329 329  {{/layout-cell}}
330 330  
331 331  {{layout-cell}}
332 -
346 +\\
333 333  
348 +\\
334 334  
350 +\\
335 335  
352 +\\
336 336  
354 +\\
337 337  
338 338  [[image:attach:safety_kamzik.PNG]]
339 339  {{/layout-cell}}
... ... @@ -352,6 +352,8 @@
352 352  * motor connected (icon green)?
353 353  )))
354 354  
373 +\\
374 +
355 355  * (((
356 356  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
357 357  
... ... @@ -360,6 +360,8 @@
360 360  * motor limits reached? → position displayed in red
361 361  )))
362 362  
383 +\\
384 +
363 363  * (((
364 364  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
365 365  
... ... @@ -368,6 +368,8 @@
368 368  * Nozzle or lines clogged? → flush with water, change nozzle
369 369  )))
370 370  
393 +\\
394 +
371 371  * (((
372 372  ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
373 373  
... ... @@ -374,15 +374,12 @@
374 374  * First, restart kamzik (server+client) and see if this solves the issue
375 375  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
376 376  * (((
377 -If nothing works, kill the Simplon process and then start the server again:*
378 -
379 -(((
401 +If nothing works, kill the Simplon process and then start the server again:* (((
380 380  (% class="code" %)
381 381  (((
382 382  ssh haspp11exp03
383 383  )))
384 384  )))
385 -
386 386  * (((
387 387  (% class="code" %)
388 388  (((
... ... @@ -396,7 +396,6 @@
396 396  )))
397 397  )))
398 398  )))
399 -* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
400 400  )))
401 401  {{/layout-cell}}
402 402  {{/layout-section}}
... ... @@ -403,7 +403,7 @@
403 403  
404 404  {{layout-section ac:type="single"}}
405 405  {{layout-cell}}
406 -
426 +\\
407 407  {{/layout-cell}}
408 408  {{/layout-section}}
409 409  {{/layout}}
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1 -https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/281980768/14. Serial Crystallography: CFEL TapeDrive