Changes for page CFEL TapeDrive: Serial Crystallography
Last modified by chatzies on 2025-11-27 11:35
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... ... @@ -1,1 +1,1 @@ 1 -1 4. Serial Crystallography: CFEL TapeDrive1 +10. Serial Crystallography: CFEL TapeDrive - Author
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... ... @@ -1,27 +1,30 @@ 1 1 {{layout}} 2 2 {{layout-section ac:type="single"}} 3 3 {{layout-cell}} 4 -[[image:attach:TapeDrive_beschriftet-tile.jpg||height=" 250"]]4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]] 5 5 6 -\\ 7 7 8 8 {{toc minLevel="2"/}} 9 9 10 -\\ 11 11 10 +---- 11 + 12 12 == {{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. 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. 15 15 16 16 Preparation: 17 17 18 -* filter through 30 µm cell filter (green) into Eppendorf or Falcon (original!) tube 18 +* 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 22 -\\ 23 23 24 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange 23 +---- 24 + 25 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}**14.2 Connecting sample to ElveFlow, sample exchange** == 26 + 27 +* 25 25 ** == 26 26 27 27 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!** ... ... @@ -38,12 +38,15 @@ 38 38 39 39 [[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]] 40 40 41 -\\ 42 42 43 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation 45 +---- 46 + 47 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}**14.3 TapeDrive operation** == 48 + 49 +* 44 44 ** == 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. 52 +The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window. 47 47 Now start the client. Same thing, a terminal will open, shortly after a small window. 48 48 49 49 Click 'Devices' in the **client session** to open the control window. ... ... @@ -51,31 +51,31 @@ 51 51 52 52 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}**Tape** ==== 53 53 54 -* Click onthe 'main tape' icon60 +* Click the 'main tape' icon 55 55 * Change the velocity by typing anything from **0.3-3.0 mm/s** 56 56 * Common velocity is 1.0-1.5 mm/s 57 57 * 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. 58 - \\64 + 59 59 * [[image:attach:kamzik_tape.PNG||height="400"]] 60 60 61 61 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}**Sample nozzle** ==== 62 62 63 -* Click an the 'nozzle' icon.69 +* Click on the 'nozzle' icon. 64 64 * ((( 65 65 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. 66 66 The absolute position is **not calibrated** and therefore changes after each restart of kamzik. 67 67 68 68 69 -(% 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" %)** !!!**(%%) 70 70 \\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. 71 71 72 72 (% class="wrapped" %) 73 73 |=((( 74 - \\80 + 75 75 )))|=((( 76 76 direction 77 77 )))|=((( 78 -recommended step size 84 +recommended step size 79 79 for visual adjustment 80 80 )))|=(% colspan="1" %)((( 81 81 recommended step size ... ... @@ -110,8 +110,8 @@ 110 110 be careful with -z, tape could be pushed out of focus 111 111 ))) 112 112 113 - **114 - \\**119 + 120 + 115 115 ))) 116 116 * [[image:attach:kamzik_nozzle.PNG||height="400"]] 117 117 ... ... @@ -119,28 +119,24 @@ 119 119 120 120 * The chiller circulates fluid through the gas nozzle. 121 121 122 -\\ 123 123 124 124 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}**Gas nozzle** ==== 125 125 126 -\\ 127 127 128 128 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}**IR camera** ==== 129 129 130 -\\ 131 131 132 132 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command: 133 133 134 134 xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611 135 - password: //written on control laptop (changes every 6 months) 136 -// 138 + password: //written on control laptop (changes every 6 months)// 137 137 138 -\\ 139 139 140 -\\ 141 141 142 - == {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Taperollexchange"/}}**14.5 Tape roll exchange** ==142 +---- 143 143 144 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}**14.4 Tape roll exchange** == 145 + 144 144 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). 145 145 146 146 * Remove the (almost) empty feeder roll by pulling it upwards. ... ... @@ -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**. //!!!BEAMSTOP!!!// 153 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!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. ... ... @@ -155,32 +155,31 @@ 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"]] 159 -** 160 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]** 160 160 161 -\\ 162 162 163 -\\ 164 164 165 -=== {{id name="14.SerialCrystallography:CFELTapeDrive-"/}}** 166 -** === 164 + 167 167 {{/layout-cell}} 168 168 {{/layout-section}} 169 169 170 170 {{layout-section ac:type="single"}} 171 171 {{layout-cell}} 172 - == {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Chopper"/}}**14.7 Chopper** ==170 +---- 173 173 172 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}**14.5 Chopper** == 173 + 174 174 start chopper gui from terminal: 175 175 176 176 (% class="code" %) 177 177 ((( 178 - cd /gpfs/local/shared/ChopperControl 178 + cd /gpfs/local/shared/ChopperControl 179 179 ))) 180 180 181 181 (% class="code" %) 182 182 ((( 183 183 python chopperControl.py 184 +\\ 184 184 ))) 185 185 {{/layout-cell}} 186 186 {{/layout-section}} ... ... @@ -193,86 +193,77 @@ 193 193 {{layout-cell}} 194 194 **Chopper → no Chopper** 195 195 196 -* decrease frequency by max. 10 Hz steps \\197 +* decrease frequency by max. 10 Hz steps 197 197 ** click arrow down 10x, "Set", arrow down 10x, "Set", .... 198 198 * at frequency = 10 Hz, click "Stop" 199 -* set "Hole" to <none> (% style="color: rgb(255,0,0);" %)//Takes some minutes//200 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes// 200 200 201 -(% style="color: rgb(0,0,0);" %)**no Chopper → Chopper**202 +(% style="color:#000000" %)**no Chopper → Chopper** 202 202 203 -* (% style="color: rgb(0,0,0);" %)set "Hole" to <Inner hole (largest)> (% style="color:rgb(255,0,0);" %)//Takes some minutes//204 -* (% style="color: rgb(0,0,0);" %)increase frequency by max. 10 Hz steps205 -** (% style="color: rgb(0,0,0);" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....206 -* (% style="color: rgb(0,0,0);" %)//usually 133Hz, results in exposure time of 3.7 ms//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// 207 207 {{/layout-cell}} 208 208 {{/layout-section}} 209 209 210 210 {{layout-section ac:type="single"}} 211 211 {{layout-cell}} 212 - == {{id name="14.SerialCrystallography:CFELTapeDrive-14.8Datacollection"/}}**14.8 Data collection** ==213 +---- 213 213 215 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}**14.6 Data collection** == 216 + 214 214 Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command: 215 215 216 216 (% class="code" %) 217 217 ((( 218 - xfreerdp +clipboard /size:1920x1080 /u: Cfelusr /v:cfeld-pcx22611221 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop 219 219 password: written on control laptop (changes every 6 months) 220 220 ))) 221 221 222 - //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//225 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password// 223 223 224 -\\ 225 - 226 -Click "Start" icon in kamzik. 227 - 228 -[[image:attach:kamzik_run-tile.jpg||height="400"]] 229 - 230 ----- 227 + 231 231 {{/layout-cell}} 232 232 {{/layout-section}} 233 233 234 -{{layout-section ac:type="two_e qual"}}231 +{{layout-section ac:type="two_left_sidebar"}} 235 235 {{layout-cell}} 236 236 **Check list:** 237 237 238 -(% style="color: rgb(255,0,0);" %)//always after entering the hutch!//235 +(% style="color:#ff0000" %)//always after entering the hutch!// 239 239 240 -* Open BS1 (//CrystalControl)// 241 -* Put collimator in (//CrystalControl)// 242 -* Check beamstop position = 27 000 (//Atk panel p11/motor/eh.3.09)// 243 -* Open fast shutter (//CrystalControl)// 244 -* Check diode voltage ~~ 0.0 (//kamzik Run/Diode voltage)// 245 -* Close fast shutter (//CrystalControl)// 237 +(% style="color:#000000" %)Click "Run" icon in kamzik. 246 246 247 -\\ 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 248 248 249 -**Set run parameters and go 🏃💥** 250 250 251 -1. Set your desired No. of frames 252 -1. Match exposure time with chopper setting 253 -1. Check trigger setting and match to chopper setting 254 -1. Set detector distance to 200.0 mm, confirm with //enter// and click "<Call>" button next to it. 255 -1. To start the run, click "<Call>" next to //exposure time// 246 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed // 256 256 257 -\\ 258 258 259 - (% style="color:rgb(153,51,102);" %)**//Currentbug~://**249 +//**Set run parameters and go 🏃💥**// 260 260 261 -(% 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>". 251 +1. Set your desired No. of frames 252 +1. Enter the protein ID of your crystal sample 253 +1. Match exposure time with chopper setting or set desired exposure time 254 +1. Check trigger setting and match to chopper setting 255 +no chopper → external triffer //off// 256 + chopper → external trigger// on// 257 +1. To start the run, click "<Call>" next to //start_run (exposure )// 258 +{{/layout-cell}} 262 262 263 - 264 -(% style="color: rgb(0,0,0);" %)Check progress in terminal with: 265 - 266 -(% class="code" %) 267 -((( 268 - cd /gpfs/current/raw/scan_frames 269 - watch "ls -lrt <run number>/ | tail" 270 -\\\\\\\\ 271 -))) 260 +{{layout-cell}} 261 +[[image:attach:Kamzik_run(2).PNG]] 272 272 {{/layout-cell}} 263 +{{/layout-section}} 273 273 265 +{{layout-section ac:type="single"}} 274 274 {{layout-cell}} 275 -(% class=" wrapped relative-table" style="width:100.0%;" %)267 +(% class="relative-table wrapped" style="width:55.9569%" %) 276 276 |=((( 277 277 Parameter 278 278 )))|=((( ... ... @@ -283,7 +283,7 @@ 283 283 |((( 284 284 Images number 285 285 )))|((( 286 - Setnumber of frames you want to collect278 +number of frames you want to collect 287 287 )))|(% colspan="1" %)((( 288 288 usually 100k - 200k, but adjust according to hitrate 289 289 ... ... @@ -294,12 +294,9 @@ 294 294 )))|((( 295 295 exposure time of Eiger 296 296 297 - \\289 + 298 298 )))|(% colspan="1" %)((( 299 -chopper at 133 Hz → 3.7 ms 300 - 301 -chopper at 66 Hz → 7.7 ms 302 - 291 +with chopper → opening time displayed in chopper GUI 303 303 no chopper → 7.7 ms 304 304 305 305 ---- ... ... @@ -309,7 +309,7 @@ 309 309 )))|((( 310 310 changes automatically 311 311 )))|(% colspan="1" %)((( 312 - \\301 + 313 313 ))) 314 314 |(% colspan="1" %)((( 315 315 Detector distance ... ... @@ -316,32 +316,49 @@ 316 316 )))|(% colspan="1" %)((( 317 317 current detector postion readout 318 318 )))|(% colspan="1" %)((( 319 - \\308 + 320 320 ))) 321 321 |(% colspan="1" %)((( 322 - move_detector (distance)311 +protein ID 323 323 )))|(% colspan="1" %)((( 324 - Setdetectordistance313 +protein ID of crystal sample (see AMARCORD) 325 325 )))|(% colspan="1" %)((( 326 - 200.0mm (% style="color: rgb(255,0,0);" %)confirm with //enter//, click "<Call>"315 + 327 327 ))) 328 -|(% colspan="1" %)((( 329 -Diode voltage 330 -)))|(% colspan="1" %)((( 331 -read out of diode 332 -)))|(% colspan="1" %)((( 333 -**~~ 0 !!! higher values indicate missaligned beam stop!!! 334 -Call local contact 335 -** 336 -))) 317 + 318 +---- 337 337 {{/layout-cell}} 338 338 {{/layout-section}} 339 339 322 +{{layout-section ac:type="two_equal"}} 323 +{{layout-cell}} 324 +**After data collection/Before entering the exp. hutch:** 325 + 326 +1. Go to "Safety" in kamzik. 327 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically: 328 +11. Drive the collimator out 329 +11. Drive the detector back to 1500 mm 330 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left). 331 + 332 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]] 333 +{{/layout-cell}} 334 + 335 +{{layout-cell}} 336 + 337 + 338 + 339 + 340 + 341 + 342 +[[image:attach:safety_kamzik.PNG]] 343 +{{/layout-cell}} 344 +{{/layout-section}} 345 + 340 340 {{layout-section ac:type="single"}} 341 341 {{layout-cell}} 342 342 ---- 343 343 344 -== {{id name="14.SerialCrystallography:CFELTapeDrive-14. 9Troubleshooting"/}}**14.9Troubleshooting** ==350 +== {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}**14.7 Troubleshooting** == 345 345 346 346 * ((( 347 347 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==== ... ... @@ -350,7 +350,6 @@ 350 350 * motor connected (icon green)? 351 351 ))) 352 352 353 -\\ 354 354 355 355 * ((( 356 356 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==== ... ... @@ -360,7 +360,6 @@ 360 360 * motor limits reached? → position displayed in red 361 361 ))) 362 362 363 -\\ 364 364 365 365 * ((( 366 366 ==== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==== ... ... @@ -369,6 +369,44 @@ 369 369 * Sample empty? 370 370 * Nozzle or lines clogged? → flush with water, change nozzle 371 371 ))) 376 + 377 + 378 +* ((( 379 +==== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==== 380 + 381 +* First, restart kamzik (server+client) and see if this solves the issue 382 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart) 383 +* ((( 384 +If nothing works, kill the Simplon process and then start the server again:* 385 + 386 +((( 387 +(% class="code" %) 388 +((( 389 +ssh haspp11exp03 390 +))) 391 +))) 392 + 393 +* ((( 394 +(% class="code" %) 395 +((( 396 +ps -ef | grep Simplon 397 +))) 398 +))) 399 +* ((( 400 +(% class="code" %) 401 +((( 402 +kill -9 simplon_process_id 403 +))) 404 +))) 405 +))) 406 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client) 407 +))) 372 372 {{/layout-cell}} 373 373 {{/layout-section}} 410 + 411 +{{layout-section ac:type="single"}} 412 +{{layout-cell}} 413 + 414 +{{/layout-cell}} 415 +{{/layout-section}} 374 374 {{/layout}}
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... ... @@ -1,1 +1,1 @@ 1 -https://confluence.desy.de/spaces/11/pages/23 6824598/14. Serial Crystallography: CFEL TapeDrive1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive