Skip to Content
Last modified by chatzies on 2025-11-27 11:35
From version 88.1
edited by chatzies
on 2025-11-27 11:35
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

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -CFEL TapeDrive: Serial Crystallography
1 +14. Serial Crystallography: CFEL TapeDrive
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.chatzies
1 +XWiki.ahenkel
Content
... ... @@ -3,28 +3,32 @@
3 3  {{layout-cell}}
4 4  [[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 5  
6 +\\
6 6  
7 -{{toc/}}
8 +{{toc minLevel="2"/}}
8 8  
10 +\\
9 9  
10 10  ----
11 11  
12 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. Sample characteristics and preparation =
14 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}**14.1 Sample characteristics and preparation** ==
13 13  
14 -* 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.
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.
15 15  
16 16  Preparation:
17 17  
18 -* filter through 30 µm (green) or 50 µm (yellow) cell filter into an Eppendorf or Falcon (original!) tube
20 +* filter through 30 µm cell filter (green) or 50 µm (yellow) into Eppendorf or Falcon (original!) tube
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"/}}8.2. Connecting sample to ElveFlow, sample exchange =
28 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange
29 +** ==
26 26  
27 -After filtration, screw the ElveFlow connector to your Eppendorf or Falcon tube. Make sure that the yellow-ish tube goes all the way 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!**
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!**
28 28  
29 29  Be aware to which channel and nozzle line your sample is connected.
30 30  
... ... @@ -38,30 +38,30 @@
38 38  
39 39  [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40 40  
45 +\\
41 41  
42 42  ----
43 43  
44 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. TapeDrive operation =
49 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation
50 +** ==
45 45  
46 -​​​​​​The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
47 -
52 +The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
48 48  Now start the client. Same thing, a terminal will open, shortly after a small window.
49 49  
50 50  Click 'Devices' in the **client session** to open the control window.
51 51  [[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
52 52  
53 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}Tape ==
58 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ====
54 54  
55 55  * Click the 'main tape' icon
56 56  * Change the velocity by typing anything from **0.3-3.0 mm/s**
57 57  * Common velocity is 1.0-1.5 mm/s
58 58  * 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 +\\
65 +* [[image:attach:kamzik_tape.PNG||height="400"]]
59 59  
60 -[[image:attach:kamzik_tape.PNG||height="400"]]
67 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ====
61 61  
62 -
63 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
64 -
65 65  * Click on the 'nozzle' icon.
66 66  * (((
67 67  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.
... ... @@ -68,16 +68,16 @@
68 68  The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
69 69  
70 70  
71 -(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving the nozzle, 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);" %)** !!!**(%%)
72 72  \\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.
73 73  
74 74  (% class="wrapped" %)
75 75  |=(((
76 -
80 +\\
77 77  )))|=(((
78 78  direction
79 79  )))|=(((
80 -recommended step size
84 +recommended step size
81 81  for visual adjustment
82 82  )))|=(% colspan="1" %)(((
83 83  recommended step size
... ... @@ -112,32 +112,38 @@
112 112  be careful with -z, tape could be pushed out of focus
113 113  )))
114 114  
115 -
119 +**
120 +\\**
116 116  )))
122 +* [[image:attach:kamzik_nozzle.PNG||height="400"]]
117 117  
118 -[[image:attach:kamzik_nozzle.PNG||height="400"]]
124 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}**Temperature control/Chiller** ====
119 119  
120 -
121 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
122 -
123 123  * The chiller circulates fluid through the gas nozzle.
124 124  
125 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
128 +\\
126 126  
130 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ====
127 127  
128 -== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
132 +\\
129 129  
134 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ====
130 130  
136 +\\
137 +
131 131  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
132 132  
133 133   xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
134 - password: //written on control laptop (changes every 6 months)//
141 + password: //written on control laptop (changes every 6 months)
142 +//
135 135  
144 +\\
136 136  
146 +\\
137 137  
138 138  ----
139 139  
140 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
150 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** ==
141 141  
142 142  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).
143 143  
... ... @@ -146,7 +146,7 @@
146 146  * Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
147 147  * Cut the first cm of the new tape roll, directly behind the black sticky part.
148 148  * 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.
149 -* 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!!!//
150 150  * Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
151 151  * Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
152 152  * Attach new tape to the empty roll by using some sticky tape.
... ... @@ -153,9 +153,15 @@
153 153  * Close tape stabilizer.
154 154  * Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
155 155  
156 -**[[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 +**
157 157  
158 -
169 +\\
170 +
171 +\\
172 +
173 +**
174 +**
159 159  {{/layout-cell}}
160 160  {{/layout-section}}
161 161  
... ... @@ -163,18 +163,19 @@
163 163  {{layout-cell}}
164 164  ----
165 165  
166 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
182 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** ==
167 167  
168 168  start chopper gui from terminal:
169 169  
170 170  (% class="code" %)
171 171  (((
172 - cd /gpfs/local/shared/ChopperControl          
188 + cd /gpfs/local/shared/ChopperControl
173 173  )))
174 174  
175 175  (% class="code" %)
176 176  (((
177 177   python chopperControl.py
194 +\\\\
178 178  )))
179 179  {{/layout-cell}}
180 180  {{/layout-section}}
... ... @@ -187,17 +187,18 @@
187 187  {{layout-cell}}
188 188  **Chopper → no Chopper**
189 189  
190 -* decrease frequency by max. 10 Hz steps
207 +* decrease frequency by max. 10 Hz steps\\
191 191  ** click arrow down 10x, "Set", arrow down 10x, "Set", ....
192 192  * at frequency = 10 Hz, click "Stop"
193 -* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
210 +* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//
194 194  
195 -(% style="color:#000000" %)**no Chopper → Chopper**
212 +(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**
196 196  
197 -* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
198 -* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
199 -** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
200 -* (% 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 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 +//
201 201  {{/layout-cell}}
202 202  {{/layout-section}}
203 203  
... ... @@ -205,7 +205,7 @@
205 205  {{layout-cell}}
206 206  ----
207 207  
208 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
226 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** ==
209 209  
210 210  Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
211 211  
... ... @@ -217,7 +217,7 @@
217 217  
218 218   //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
219 219  
220 -
238 +\\
221 221  {{/layout-cell}}
222 222  {{/layout-section}}
223 223  
... ... @@ -225,18 +225,23 @@
225 225  {{layout-cell}}
226 226  **Check list:**
227 227  
228 -(% style="color:#ff0000" %)//always after entering the hutch!//
246 +(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//
229 229  
230 -(% style="color:#000000" %)Click "Run" icon in kamzik.
248 +(% style="color: rgb(0,0,0);" %)Click "Run" icon in kamzik.
231 231  
232 -* Put detector distance 200 mm in //prepare_for_measurement (      )//
233 -* Click "<Call>" next to //prepare_for_measurement//
234 -This will:
250 +* Put detector distance 200 in //prepare_for_measurement (      )
251 +//
252 +* Click "<Call>" next to //prepare_for_measurement
253 +//This will:\\
235 235  ** drive the collimator in //IN// position
236 236  ** drive detector to 200 mm
237 237  
238 -* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
257 +\\
239 239  
259 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
260 +
261 +\\
262 +
240 240  //**Set run parameters and go 🏃💥**//
241 241  
242 242  1. Set your desired No. of frames
... ... @@ -243,8 +243,9 @@
243 243  1. Enter the protein ID of your crystal sample
244 244  1. Match exposure time with chopper setting or set desired exposure time
245 245  1. Check trigger setting and match to chopper setting
246 -no chopper → external triffer //off//
247 - chopper → external trigger// on//
269 +no chopper → external triffer //off
270 +// chopper → external trigger// on
271 +//
248 248  1. To start the run, click "<Call>" next to //start_run (exposure    )//
249 249  {{/layout-cell}}
250 250  
... ... @@ -255,7 +255,7 @@
255 255  
256 256  {{layout-section ac:type="single"}}
257 257  {{layout-cell}}
258 -(% class="relative-table wrapped" style="width:55.9569%" %)
282 +(% class="relative-table wrapped" style="width: 55.9569%;" %)
259 259  |=(((
260 260  Parameter
261 261  )))|=(((
... ... @@ -277,7 +277,7 @@
277 277  )))|(((
278 278  exposure time of Eiger
279 279  
280 -
304 +\\
281 281  )))|(% colspan="1" %)(((
282 282  with chopper         → opening time displayed in chopper GUI
283 283  no chopper            → 7.7 ms
... ... @@ -289,7 +289,7 @@
289 289  )))|(((
290 290  changes automatically
291 291  )))|(% colspan="1" %)(((
292 -
316 +\\
293 293  )))
294 294  |(% colspan="1" %)(((
295 295  Detector distance
... ... @@ -296,7 +296,7 @@
296 296  )))|(% colspan="1" %)(((
297 297  current detector postion readout
298 298  )))|(% colspan="1" %)(((
299 -
323 +\\
300 300  )))
301 301  |(% colspan="1" %)(((
302 302  protein ID
... ... @@ -303,7 +303,7 @@
303 303  )))|(% colspan="1" %)(((
304 304  protein ID of crystal sample (see AMARCORD)
305 305  )))|(% colspan="1" %)(((
306 -
330 +\\
307 307  )))
308 308  
309 309  ----
... ... @@ -324,8 +324,16 @@
324 324  {{/layout-cell}}
325 325  
326 326  {{layout-cell}}
327 -
351 +\\
328 328  
353 +\\
354 +
355 +\\
356 +
357 +\\
358 +
359 +\\
360 +
329 329  [[image:attach:safety_kamzik.PNG]]
330 330  {{/layout-cell}}
331 331  {{/layout-section}}
... ... @@ -334,17 +334,19 @@
334 334  {{layout-cell}}
335 335  ----
336 336  
337 -= {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
369 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** ==
338 338  
339 339  * (((
340 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
372 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ====
341 341  
342 342  * Tape roll empty?
343 343  * motor connected (icon green)?
344 344  )))
345 345  
378 +\\
379 +
346 346  * (((
347 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
381 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ====
348 348  
349 349  * displayed in green=connected?
350 350  * nozzle holder colliding somewhere?
... ... @@ -351,8 +351,10 @@
351 351  * motor limits reached? → position displayed in red
352 352  )))
353 353  
388 +\\
389 +
354 354  * (((
355 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
391 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ====
356 356  
357 357  * channel turned on?
358 358  * Sample empty?
... ... @@ -359,21 +359,20 @@
359 359  * Nozzle or lines clogged? → flush with water, change nozzle
360 360  )))
361 361  
398 +\\
399 +
362 362  * (((
363 -== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
401 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ====
364 364  
365 365  * First, restart kamzik (server+client) and see if this solves the issue
366 366  * If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
367 367  * (((
368 -If nothing works, kill the Simplon process and then start the server again:*
369 -
370 -(((
406 +If nothing works, kill the Simplon process and then start the server again:* (((
371 371  (% class="code" %)
372 372  (((
373 373  ssh haspp11exp03
374 374  )))
375 375  )))
376 -
377 377  * (((
378 378  (% class="code" %)
379 379  (((
... ... @@ -391,4 +391,10 @@
391 391  )))
392 392  {{/layout-cell}}
393 393  {{/layout-section}}
429 +
430 +{{layout-section ac:type="single"}}
431 +{{layout-cell}}
432 +\\
433 +{{/layout-cell}}
434 +{{/layout-section}}
394 394  {{/layout}}
XWiki.XWikiRights[0]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view,comment,edit
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.ahenkel
XWiki.XWikiRights[1]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view,comment,edit,delete
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.chatzies
XWiki.XWikiRights[2]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Levels
... ... @@ -1,1 +1,0 @@
1 -view
Users
... ... @@ -1,1 +1,0 @@
1 -XWiki.XWikiGuest