Opened 17 months ago
Last modified 17 months ago
#15403 assigned defect
ISOLDE tug: Assertion failure at CustomExternalForce.cpp:104. Index out of range
Reported by: | Owned by: | Tristan Croll | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Linux-5.13.0-28-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /data/lukas/hnRNPA1A/hnRNPA1m/isolde/hnRNAPA1_10.cxs Opened postprocess_masked_job250.mrc as #2, grid size 256,256,256, pixel 1.3, shown at level 0.0218, step 1, values float32 Log from Tue Jun 11 01:13:06 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/lukas/hnRNPA1A/For_Peter/hnRNPA1A_joined_1.pdb Chain information for hnRNPA1A_joined_1.pdb #1 --- Chain | Description A | No description available > open /data/lukas/hnRNPA1A/For_Peter/globular-cterminus.pdb Chain information for globular-cterminus.pdb #2 --- Chain | Description A | No description available > select #2:298 A@C #1:349 A@N Expected a keyword > select #2:298@C #1:349@N 2 atoms, 2 residues, 2 models selected > select add #1 2569 atoms, 2616 bonds, 298 residues, 2 models selected > select subtract #1 1 atom, 1 residue, 1 model selected > select add #2 168 atoms, 171 bonds, 23 residues, 1 model selected > ui mousemode right "translate selected models" > view matrix models > #2,0.99468,-0.037505,-0.095952,8.3351,0.035105,0.99903,-0.026574,3.5077,0.096855,0.023064,0.99503,3.6163 > select subtract #2 Nothing selected > select #2:298@C #1:349@N 2 atoms, 2 residues, 2 models selected > ui tool show "Build Structure" > build join peptide sel length 1.33 omega 180 phi -120 move small No chain-terminal carbons in atoms > build join peptide sel length 1.33 omega 180 phi -120 move small No chain-terminal carbons in atoms > select #2:298@N #1:349@C 2 atoms, 2 residues, 2 models selected > build join peptide sel length 1.33 omega 180 phi -120 move small > open /data/lukas/hnRNPA1A/hnRNPA1m/isolde/postprocess_masked_job250.mrc Opened postprocess_masked_job250.mrc as #2, grid size 256,256,256, pixel 1.3, shown at level 0.00323, step 1, values float32 > volume #2 level 0.02183 > select add #1 2736 atoms, 2788 bonds, 320 residues, 1 model selected > view matrix models > #1,0.99808,-0.020842,-0.058254,2.2569,0.018187,0.99879,-0.045735,1.3182,0.059136,0.044588,0.99725,-1.2581 > view matrix models > #1,0.99808,-0.020842,-0.058254,208.94,0.018187,0.99879,-0.045735,106.87,0.059136,0.044588,0.99725,32.64 > view matrix models > #1,-0.11866,-0.85268,0.50878,214.51,-0.73223,0.42123,0.53517,103.75,-0.67064,-0.30904,-0.67434,106.4 > view matrix models > #1,-0.12756,-0.8573,0.49876,215.05,-0.73909,0.41751,0.52861,104.13,-0.66141,-0.3012,-0.68689,106.63 > view matrix models > #1,-0.21586,-0.90033,0.37791,221.12,-0.80835,0.38187,0.44804,108.4,-0.5477,-0.20877,-0.81021,108.3 > view matrix models > #1,-0.38125,-0.92438,0.013173,236.86,-0.8126,0.34188,0.47202,107.97,-0.44083,0.16925,-0.88149,105.8 > view matrix models > #1,-0.38125,-0.92438,0.013173,255.64,-0.8126,0.34188,0.47202,106.75,-0.44083,0.16925,-0.88149,181.67 > view matrix models > #1,0.1964,-0.95734,0.21195,239.44,-0.49476,0.089871,0.86437,89.892,-0.84655,-0.27462,-0.456,177.19 > view matrix models > #1,0.091232,-0.9353,0.3419,236.41,-0.42469,0.274,0.86288,87.215,-0.90073,-0.22393,-0.37221,174.71 > view matrix models > #1,0.091232,-0.9353,0.3419,168.01,-0.42469,0.274,0.86288,93.995,-0.90073,-0.22393,-0.37221,184.83 > transparency 50 > view matrix models > #1,0.091232,-0.9353,0.3419,193.05,-0.42469,0.274,0.86288,133.92,-0.90073,-0.22393,-0.37221,184.28 > view matrix models > #1,0.4871,0.30029,-0.8201,216.78,-0.32466,0.934,0.14916,151.7,0.81076,0.19359,0.55244,120.07 > view matrix models > #1,0.4871,0.30029,-0.8201,207.47,-0.32466,0.934,0.14916,123.07,0.81076,0.19359,0.55244,122.78 > view matrix models > #1,0.4871,0.30029,-0.8201,214,-0.32466,0.934,0.14916,129.52,0.81076,0.19359,0.55244,122.04 > ui tool show "Fit in Map" > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005304, steps = 684 shifted from previous position = 7.15 rotated from previous position = 5.02 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54373646 0.33720874 -0.76853167 207.17738351 -0.32072171 0.92971461 0.18102026 132.02822557 0.77555673 0.14805747 0.61366989 116.87211109 Axis -0.01963543 -0.91979008 -0.39191920 Axis point 52.46428299 0.00000000 234.05162308 Rotation angle (degrees) 57.07365317 Shift along axis -171.31069419 Average map value = 0.005304 for 2736 atoms, 2486 outside contour > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005317, steps = 60 shifted from previous position = 0.388 rotated from previous position = 0.456 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54539011 0.34346794 -0.76457792 206.78232430 -0.32213951 0.92801910 0.18710075 131.63679840 0.77380602 0.14425785 0.61677703 116.72267243 Axis -0.02555114 -0.91747906 -0.39696260 Axis point 53.05809824 0.00000000 233.14402554 Rotation angle (degrees) 56.96897241 Shift along axis -172.39206660 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005326, steps = 48 shifted from previous position = 0.243 rotated from previous position = 0.274 degrees atoms outside contour = 2484, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54506893 0.34729735 -0.76307562 206.59200087 -0.32240471 0.92700609 0.19161138 131.34245680 0.77392187 0.14157776 0.61725252 116.72727954 Axis -0.02982969 -0.91634725 -0.39927172 Axis point 53.31692584 0.00000000 232.18176526 Rotation angle (degrees) 56.99831025 Shift along axis -173.12377714 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005322, steps = 48 shifted from previous position = 0.149 rotated from previous position = 0.179 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54637583 0.34465230 -0.76334019 206.66862223 -0.32157956 0.92787639 0.18876437 131.52071661 0.77334341 0.14233831 0.61780237 116.67946327 Axis -0.02770820 -0.91713024 -0.39762342 Axis point 53.06276292 0.00000000 232.93898090 Rotation angle (degrees) 56.90510655 Shift along axis -172.74252932 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005319, steps = 108 shifted from previous position = 0.0734 rotated from previous position = 0.0944 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54610267 0.34354893 -0.76403272 206.73812777 -0.32174845 0.92810445 0.18735009 131.61212325 0.77346609 0.14351396 0.61737666 116.69005569 Axis -0.02615768 -0.91744881 -0.39699302 Axis point 53.01619594 0.00000000 233.18704481 Rotation angle (degrees) 56.92120449 Shift along axis -172.48031366 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005319, steps = 108 shifted from previous position = 0.124 rotated from previous position = 0.169 degrees atoms outside contour = 2485, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54393546 0.34458185 -0.76511278 206.79067241 -0.32152397 0.92779282 0.18926919 131.49038194 0.77508487 0.14305188 0.61545073 116.82451861 Axis -0.02753157 -0.91749296 -0.39679803 Axis point 53.01486110 0.00000000 232.45989101 Rotation angle (degrees) 57.07167205 Shift along axis -172.69051034 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005321, steps = 108 shifted from previous position = 0.104 rotated from previous position = 0.121 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54349411 0.34654002 -0.76454180 206.71266026 -0.32235788 0.92713202 0.19108013 131.37549169 0.77504810 0.14260515 0.61560069 116.82392933 Axis -0.02886586 -0.91679435 -0.39831504 Axis point 53.24065708 0.00000000 232.05508129 Rotation angle (degrees) 57.10416523 Shift along axis -172.94397582 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005318, steps = 96 shifted from previous position = 0.173 rotated from previous position = 0.235 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54588983 0.34329559 -0.76429865 206.75767693 -0.32087864 0.92831787 0.18778399 131.58260188 0.77397752 0.14273774 0.61691550 116.73473218 Axis -0.02687497 -0.91774842 -0.39625190 Axis point 52.87075483 0.00000000 233.03801751 Rotation angle (degrees) 56.93695007 Shift along axis -172.57269140 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005312, steps = 44 shifted from previous position = 0.124 rotated from previous position = 0.152 degrees atoms outside contour = 2488, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54707529 0.34192792 -0.76406409 206.77638862 -0.32148698 0.92859263 0.18536948 131.74648807 0.77288728 0.14422560 0.61793545 116.65391328 Axis -0.02457049 -0.91784357 -0.39618111 Axis point 52.89056919 0.00000000 233.73619021 Rotation angle (degrees) 56.85212927 Shift along axis -172.21934158 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00532, steps = 44 shifted from previous position = 0.174 rotated from previous position = 0.201 degrees atoms outside contour = 2484, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54760446 0.34468582 -0.76244412 206.60735328 -0.32192752 0.92785993 0.18825146 131.55976254 0.77232896 0.14236440 0.61906409 116.60192656 Axis -0.02741294 -0.91687374 -0.39823494 Axis point 53.12994963 0.00000000 233.24564881 Rotation angle (degrees) 56.82046964 Shift along axis -172.72236798 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005321, steps = 96 shifted from previous position = 0.0852 rotated from previous position = 0.115 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54668225 0.34452796 -0.76317691 206.65103806 -0.32068757 0.92808464 0.18925744 131.48843460 0.77349725 0.14127766 0.61785324 116.69591338 Axis -0.02864180 -0.91732648 -0.39710423 Axis point 52.92582658 0.00000000 232.85205074 Rotation angle (degrees) 56.88576541 Shift along axis -172.87712276 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00532, steps = 80 shifted from previous position = 0.0855 rotated from previous position = 0.12 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54827447 0.34428484 -0.76214372 206.58919697 -0.32103915 0.92815261 0.18832578 131.54702921 0.77222339 0.14142375 0.61941129 116.59207347 Axis -0.02803363 -0.91710087 -0.39766833 Axis point 52.98554612 0.00000000 233.30259634 Rotation angle (degrees) 56.77562255 Shift along axis -172.79831690 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 116 shifted from previous position = 0.0366 rotated from previous position = 0.0649 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54733827 0.34456682 -0.76268901 206.62025609 -0.32115595 0.92801906 0.18878420 131.51728284 0.77283871 0.14161329 0.61860003 116.63728882 Axis -0.02817363 -0.91712004 -0.39761424 Axis point 53.00908724 0.00000000 233.06517189 Rotation angle (degrees) 56.84001585 Shift along axis -172.81502540 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 40 shifted from previous position = 0.0947 rotated from previous position = 0.112 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54644615 0.34596811 -0.76269435 206.59350515 -0.32122949 0.92761655 0.19062830 131.39520487 0.77343921 0.14083181 0.61802765 116.68739168 Axis -0.02972018 -0.91681472 -0.39820533 Axis point 53.08906475 0.00000000 232.55851774 Rotation angle (degrees) 56.90388350 Shift along axis -173.07059468 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005317, steps = 104 shifted from previous position = 0.264 rotated from previous position = 0.303 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54724447 0.34163639 -0.76407334 206.77450861 -0.32074056 0.92880997 0.18557353 131.72708352 0.77307761 0.14351522 0.61786276 116.65937461 Axis -0.02511965 -0.91807514 -0.39560970 Axis point 52.77235380 0.00000000 233.68685281 Rotation angle (degrees) 56.84139077 Shift along axis -172.28104374 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005319, steps = 104 shifted from previous position = 0.198 rotated from previous position = 0.231 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54650554 0.34480957 -0.76317629 206.64662168 -0.32087547 0.92797243 0.18948905 131.47721807 0.77354420 0.14132773 0.61778301 116.70491869 Axis -0.02874616 -0.91722590 -0.39732896 Axis point 52.96427353 0.00000000 232.78666890 Rotation angle (degrees) 56.89804858 Shift along axis -172.90485119 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005328, steps = 64 shifted from previous position = 0.152 rotated from previous position = 0.18 degrees atoms outside contour = 2484, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54572780 0.34751289 -0.76250637 206.54981079 -0.32150746 0.92714532 0.19244350 131.28711546 0.77383081 0.14012972 0.61769696 116.71719848 Axis -0.03120414 -0.91639482 -0.39905744 Axis point 53.21534297 0.00000000 232.08574188 Rotation angle (degrees) 56.95585543 Shift along axis -173.33290712 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005327, steps = 84 shifted from previous position = 0.0759 rotated from previous position = 0.114 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54726279 0.34779400 -0.76127706 206.45436615 -0.32144527 0.92715562 0.19249777 131.27652772 0.77277188 0.13936204 0.61919451 116.63071931 Axis -0.03173195 -0.91611370 -0.39966082 Axis point 53.24184294 0.00000000 232.30253133 Rotation angle (degrees) 56.85180249 Shift along axis -173.42815438 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00532, steps = 116 shifted from previous position = 0.237 rotated from previous position = 0.272 degrees atoms outside contour = 2488, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54752897 0.34383765 -0.76288118 206.64412724 -0.32081879 0.92826966 0.18812429 131.55982449 0.77284367 0.14174311 0.61856411 116.64185723 Axis -0.02770633 -0.91738294 -0.39704018 Axis point 52.91480736 0.00000000 233.21595263 Rotation angle (degrees) 56.82614309 Shift along axis -172.72759371 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005322, steps = 68 shifted from previous position = 0.154 rotated from previous position = 0.225 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54450983 0.34539619 -0.76433665 206.71658609 -0.32097552 0.92771748 0.19056493 131.40768749 0.77490887 0.14156887 0.61601501 116.80989376 Axis -0.02919885 -0.91730234 -0.39711944 Axis point 52.99188058 0.00000000 232.26539820 Rotation angle (degrees) 57.03537293 Shift along axis -172.96394482 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005325, steps = 80 shifted from previous position = 0.135 rotated from previous position = 0.193 degrees atoms outside contour = 2488, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54715677 0.34567525 -0.76231757 206.57375077 -0.32120513 0.92772642 0.19013402 131.43028085 0.77294678 0.14082720 0.61864446 116.64301112 Axis -0.02944440 -0.91680904 -0.39823888 Axis point 53.08334611 0.00000000 232.76458260 Rotation angle (degrees) 56.85471983 Shift along axis -173.03069254 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 60 shifted from previous position = 0.0638 rotated from previous position = 0.0835 degrees atoms outside contour = 2485, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54804165 0.34520581 -0.76189454 206.55379838 -0.32160350 0.92781065 0.18904653 131.50555589 0.77215383 0.14142258 0.61949828 116.58343679 Axis -0.02845970 -0.91673535 -0.39848005 Axis point 53.12194675 0.00000000 233.13525854 Rotation angle (degrees) 56.79232613 Shift along axis -172.89042444 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005311, steps = 52 shifted from previous position = 0.212 rotated from previous position = 0.244 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54909127 0.34183357 -0.76265889 206.68086413 -0.32135690 0.92873086 0.18490195 131.77606232 0.77151054 0.14355764 0.61980858 116.53894588 Axis -0.02472913 -0.91762736 -0.39667178 Axis point 52.89635920 0.00000000 234.14083958 Rotation angle (degrees) 56.71422047 Shift along axis -172.26006818 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005319, steps = 136 shifted from previous position = 0.179 rotated from previous position = 0.219 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54696379 0.34408144 -0.76317663 206.66484567 -0.32113016 0.92812676 0.18829799 131.55005420 0.77311450 0.14208685 0.61814666 116.66535668 Axis -0.02759264 -0.91731832 -0.39719737 Axis point 52.96736950 0.00000000 233.10861823 Rotation angle (degrees) 56.86465704 Shift along axis -172.71487513 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005326, steps = 160 shifted from previous position = 0.169 rotated from previous position = 0.202 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54918802 0.34559278 -0.76089299 206.46947903 -0.32175231 0.92773940 0.18914292 131.49046896 0.77127684 0.14094405 0.62069864 116.50196539 Axis -0.02882897 -0.91642967 -0.39915604 Axis point 53.18561873 0.00000000 233.28721312 Rotation angle (degrees) 56.71437988 Shift along axis -172.95653301 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005322, steps = 120 shifted from previous position = 0.131 rotated from previous position = 0.183 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54665087 0.34540423 -0.76280321 206.61001567 -0.32173772 0.92767349 0.18949074 131.47701450 0.77308322 0.14183729 0.61824309 116.66127288 Axis -0.02844642 -0.91683743 -0.39824606 Axis point 53.12929840 0.00000000 232.83340631 Rotation angle (degrees) 56.88756760 Shift along axis -172.88025480 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005317, steps = 60 shifted from previous position = 0.0511 rotated from previous position = 0.0686 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54707198 0.34431265 -0.76299479 206.64798020 -0.32095904 0.92810596 0.18869188 131.52152202 0.77310901 0.14166203 0.61825102 116.66877612 Axis -0.02808359 -0.91727503 -0.39726293 Axis point 52.95438639 0.00000000 233.04327756 Rotation angle (degrees) 56.85809686 Shift along axis -172.79300511 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00532, steps = 80 shifted from previous position = 0.122 rotated from previous position = 0.141 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54803169 0.34303010 -0.76288375 206.66918021 -0.32158577 0.92834921 0.18641442 131.67281659 0.77216828 0.14317154 0.61907839 116.58177184 Axis -0.02584271 -0.91737414 -0.39718615 Axis point 52.99131230 0.00000000 233.66928781 Rotation angle (degrees) 56.78860367 Shift along axis -172.43879321 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 48 shifted from previous position = 0.165 rotated from previous position = 0.208 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54619336 0.34511964 -0.76325962 206.64775596 -0.32115000 0.92783104 0.18971620 131.46776633 0.77365075 0.14149909 0.61761032 116.70670469 Axis -0.02877245 -0.91711584 -0.39758105 Axis point 53.02562861 0.00000000 232.69817322 Rotation angle (degrees) 56.91946289 Shift along axis -172.91730635 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005319, steps = 64 shifted from previous position = 0.0951 rotated from previous position = 0.117 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54671467 0.34362319 -0.76356151 206.70226848 -0.32124345 0.92820746 0.18770603 131.59266649 0.77324363 0.14266750 0.61785133 116.67684219 Axis -0.02688762 -0.91745945 -0.39691966 Axis point 52.95404070 0.00000000 233.19427933 Rotation angle (degrees) 56.88052115 Shift along axis -172.59999911 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 48 shifted from previous position = 0.127 rotated from previous position = 0.151 degrees atoms outside contour = 2485, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54565751 0.34550498 -0.76346853 206.66341140 -0.32123515 0.92769519 0.19023566 131.41954114 0.77399345 0.14144941 0.61719219 116.72938512 Axis -0.02909975 -0.91705677 -0.39769345 Axis point 53.05695537 0.00000000 232.52355940 Rotation angle (degrees) 56.95671634 Shift along axis -172.95554500 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 164 shifted from previous position = 0.0535 rotated from previous position = 0.076 degrees atoms outside contour = 2483, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54602953 0.34611139 -0.76292769 206.61264365 -0.32229088 0.92736762 0.19004705 131.44292463 0.77329189 0.14211333 0.61791865 116.67874241 Axis -0.02859980 -0.91659001 -0.39880422 Axis point 53.24509873 0.00000000 232.65042903 Rotation angle (degrees) 56.93036631 Shift along axis -172.92032657 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00533, steps = 80 shifted from previous position = 0.192 rotated from previous position = 0.234 degrees atoms outside contour = 2484, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54688319 0.34871973 -0.76112635 206.42522981 -0.32177143 0.92684484 0.19344711 131.21454529 0.77290486 0.13911574 0.61908391 116.63809995 Axis -0.03243585 -0.91581716 -0.40028345 Axis point 53.34053967 0.00000000 232.05925593 Rotation angle (degrees) 56.87920468 Shift along axis -173.55241079 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 224 shifted from previous position = 0.0992 rotated from previous position = 0.273 degrees atoms outside contour = 2492, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.55005447 0.34881732 -0.75879283 206.25855200 -0.31943517 0.92737882 0.19475547 131.10760363 0.77162248 0.13525900 0.62153339 116.53807916 Axis -0.03560511 -0.91586281 -0.39990949 Axis point 53.05213104 0.00000000 232.20013785 Rotation angle (degrees) 56.66842490 Shift along axis -174.02511954 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005329, steps = 104 shifted from previous position = 0.166 rotated from previous position = 0.343 degrees atoms outside contour = 2484, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54622769 0.34801391 -0.76191970 206.50216840 -0.32190757 0.92696917 0.19262311 131.27737625 0.77331159 0.14005165 0.61836455 116.67295590 Axis -0.03136991 -0.91608778 -0.39974881 Axis point 53.31319201 0.00000000 232.13892611 Rotation angle (degrees) 56.92196945 Shift along axis -173.37943028 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 120 shifted from previous position = 0.126 rotated from previous position = 0.163 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54742060 0.34553311 -0.76219259 206.56225594 -0.32093360 0.92782328 0.19011993 131.43444688 0.77287276 0.14053765 0.61880276 116.64319263 Axis -0.02961489 -0.91687583 -0.39807245 Axis point 53.03324265 0.00000000 232.79599667 Rotation angle (degrees) 56.83696088 Shift along axis -173.05882722 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005316, steps = 84 shifted from previous position = 0.26 rotated from previous position = 0.304 degrees atoms outside contour = 2485, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54846011 0.34163066 -0.76320377 206.71756853 -0.32121336 0.92877828 0.18491317 131.77243888 0.77201910 0.14373374 0.61913417 116.57239987 Axis -0.02461835 -0.91780437 -0.39626894 Axis point 52.85822991 0.00000000 234.02673649 Rotation angle (degrees) 56.75732706 Shift along axis -172.22438779 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005314, steps = 72 shifted from previous position = 0.143 rotated from previous position = 0.19 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54596452 0.34132334 -0.76512817 206.85240117 -0.32052450 0.92886838 0.18565446 131.72104720 0.77407156 0.14388157 0.61653168 116.74480947 Axis -0.02492439 -0.91838553 -0.39490098 Axis point 52.70214694 0.00000000 233.46553100 Rotation angle (degrees) 56.92869867 Shift along axis -172.22901418 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00532, steps = 96 shifted from previous position = 0.147 rotated from previous position = 0.18 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54736367 0.34334318 -0.76322243 206.68277904 -0.32113075 0.92832644 0.18731007 131.61407519 0.77283119 0.14256746 0.61839022 116.63837895 Axis -0.02672456 -0.91747817 -0.39688740 Axis point 52.93219136 0.00000000 233.36829699 Rotation angle (degrees) 56.83580838 Shift along axis -172.56885091 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005313, steps = 44 shifted from previous position = 0.119 rotated from previous position = 0.137 degrees atoms outside contour = 2488, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54647666 0.34167856 -0.76460383 206.81667983 -0.32070146 0.92877235 0.18582922 131.70764792 0.77363676 0.14365823 0.61712922 116.71162881 Axis -0.02517184 -0.91817510 -0.39537433 Axis point 52.75586563 0.00000000 233.52488507 Rotation angle (degrees) 56.89403886 Shift along axis -172.28142210 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005315, steps = 96 shifted from previous position = 0.0218 rotated from previous position = 0.0277 degrees atoms outside contour = 2488, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54638276 0.34136766 -0.76480978 206.83255947 -0.32076654 0.92883148 0.18542090 131.73788830 0.77367610 0.14401460 0.61699683 116.71180971 Axis -0.02471380 -0.91826178 -0.39520189 Axis point 52.74693936 0.00000000 233.58719222 Rotation angle (degrees) 56.89975553 Shift along axis -172.20621350 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005321, steps = 80 shifted from previous position = 0.197 rotated from previous position = 0.23 degrees atoms outside contour = 2486, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54571579 0.34459940 -0.76383606 206.71002386 -0.32101450 0.92796327 0.18929834 131.47919127 0.77404390 0.14189935 0.61702561 116.73544918 Axis -0.02827404 -0.91736297 -0.39704630 Axis point 52.97237582 0.00000000 232.71947750 Rotation angle (degrees) 56.95125550 Shift along axis -172.80804643 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005323, steps = 160 shifted from previous position = 0.0557 rotated from previous position = 0.0687 degrees atoms outside contour = 2485, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54590201 0.34539672 -0.76334271 206.65121290 -0.32199711 0.92759351 0.18944163 131.48454300 0.77350427 0.14237758 0.61759191 116.69541228 Axis -0.02807841 -0.91688302 -0.39816721 Axis point 53.15827632 0.00000000 232.73892182 Rotation angle (degrees) 56.93817267 Shift along axis -172.82266951 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005326, steps = 44 shifted from previous position = 0.135 rotated from previous position = 0.177 degrees atoms outside contour = 2485, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54814162 0.34599299 -0.76146544 206.51341687 -0.32272044 0.92741468 0.18908602 131.51265364 0.77161667 0.14209455 0.62001359 116.53629168 Axis -0.02808415 -0.91623653 -0.39965222 Axis point 53.33788675 0.00000000 233.17844352 Rotation angle (degrees) 56.78481666 Shift along axis -172.87043902 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005327, steps = 96 shifted from previous position = 0.0704 rotated from previous position = 0.114 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54832750 0.34625515 -0.76121241 206.48702331 -0.32133782 0.92761061 0.19047455 131.40569857 0.77206150 0.14016390 0.61989928 116.56802729 Axis -0.03007098 -0.91644710 -0.39902437 Axis point 53.15685299 0.00000000 232.87950853 Rotation angle (degrees) 56.77565644 Shift along axis -173.14912144 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005313, steps = 80 shifted from previous position = 0.26 rotated from previous position = 0.3 degrees atoms outside contour = 2487, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.54706025 0.34230159 -0.76390752 206.75637596 -0.32060814 0.92866419 0.18652946 131.65997793 0.77326289 0.14287212 0.61777994 116.68411019 Axis -0.02607049 -0.91793894 -0.39586415 Axis point 52.78427003 0.00000000 233.47428418 Rotation angle (degrees) 56.85551642 Shift along axis -172.43711643 > view matrix models > #1,0.50737,0.59849,-0.61999,200.16,-0.72898,0.68176,0.061572,144.88,0.45954,0.42072,0.78219,113.69 > view matrix models > #1,0.50737,0.59849,-0.61999,213.82,-0.72898,0.68176,0.061572,154.53,0.45954,0.42072,0.78219,142.33 > view matrix models > #1,0.32135,0.52309,-0.78937,223.48,-0.84857,0.52906,0.0051418,159.78,0.42031,0.66818,0.6139,146.77 > view matrix models > #1,0.32135,0.52309,-0.78937,205.7,-0.84857,0.52906,0.0051418,146.73,0.42031,0.66818,0.6139,155.17 > view matrix models > #1,0.32135,0.52309,-0.78937,206.63,-0.84857,0.52906,0.0051418,152.83,0.42031,0.66818,0.6139,155.43 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.006728, steps = 2000 shifted from previous position = 3.07 rotated from previous position = 10.8 degrees atoms outside contour = 2388, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.43214605 0.49364630 -0.75469405 204.93272015 -0.74074670 0.67161373 0.01514372 148.82569656 0.51433853 0.55249283 0.65590209 152.10228853 Axis 0.29044142 -0.68592209 -0.66719912 Axis point 73.09018212 0.00000000 271.98389751 Rotation angle (degrees) 67.67678929 Shift along axis -144.04439547 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.006775, steps = 2000 shifted from previous position = 0.542 rotated from previous position = 0.528 degrees atoms outside contour = 2389, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.43041887 0.48740977 -0.75971791 205.49283661 -0.74163007 0.67073232 0.01014838 149.29634865 0.51451377 0.55906159 0.65017360 152.30045990 Axis 0.29614746 -0.68746838 -0.66308666 Axis point 72.68330257 0.00000000 271.64608861 Rotation angle (degrees) 67.93474114 Shift along axis -142.76874000 > view matrix models > #1,0.41779,0.44972,-0.78944,207.07,-0.74745,0.66409,-0.017257,150.41,0.5165,0.59728,0.61359,153.23 > view matrix models > #1,0.41779,0.44972,-0.78944,215.71,-0.74745,0.66409,-0.017257,146.1,0.5165,0.59728,0.61359,126.92 > view matrix models > #1,0.41779,0.44972,-0.78944,212.35,-0.74745,0.66409,-0.017257,154.33,0.5165,0.59728,0.61359,126.28 > view matrix models > #1,0.41779,0.44972,-0.78944,213.53,-0.74745,0.66409,-0.017257,150.99,0.5165,0.59728,0.61359,125.16 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005525, steps = 304 shifted from previous position = 2.01 rotated from previous position = 8.16 degrees atoms outside contour = 2457, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.50553596 0.38604391 -0.77162393 210.45405412 -0.64859269 0.75981641 -0.04479440 152.03996587 0.56899992 0.52311482 0.63449978 124.12209797 Axis 0.31795486 -0.75057395 -0.57926113 Axis point 77.80412652 0.00000000 271.96097797 Rotation angle (degrees) 63.26105862 Shift along axis -119.10145515 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005529, steps = 80 shifted from previous position = 0.168 rotated from previous position = 0.327 degrees atoms outside contour = 2458, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.50916651 0.38753451 -0.76848323 210.22282754 -0.64636936 0.76174800 -0.04412067 151.93241473 0.56829228 0.51918878 0.63834700 123.92357519 Axis 0.31622437 -0.75042411 -0.58040141 Axis point 77.72255201 -0.00000000 273.07122914 Rotation angle (degrees) 62.95882139 Shift along axis -119.46158379 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005528, steps = 84 shifted from previous position = 0.0823 rotated from previous position = 0.125 degrees atoms outside contour = 2459, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.50920241 0.38812104 -0.76816337 210.22019530 -0.64539639 0.76266574 -0.04247895 151.80046818 0.56936491 0.51740025 0.63884316 123.90927337 Axis 0.31442949 -0.75115906 -0.58042585 Axis point 77.74678306 0.00000000 273.04829441 Rotation angle (degrees) 62.91217976 Shift along axis -119.84701277 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005528, steps = 84 shifted from previous position = 0.0303 rotated from previous position = 0.0489 degrees atoms outside contour = 2455, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.50856130 0.38793075 -0.76868403 210.25749397 -0.64560099 0.76250145 -0.04231897 151.79704664 0.56970586 0.51778496 0.63822721 123.94682736 Axis 0.31442746 -0.75133650 -0.58019724 Axis point 77.75745669 -0.00000000 272.84255459 Rotation angle (degrees) 62.95790599 Shift along axis -119.85353990 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00553, steps = 64 shifted from previous position = 0.0859 rotated from previous position = 0.116 degrees atoms outside contour = 2458, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51004065 0.38828700 -0.76752312 210.17019304 -0.64560024 0.76244698 -0.04330047 151.85131822 0.56838267 0.51759811 0.63955713 123.85775349 Axis 0.31512279 -0.75053560 -0.58085621 Axis point 77.73915227 0.00000000 273.34200409 Rotation angle (degrees) 62.86926463 Shift along axis -119.68394897 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005529, steps = 48 shifted from previous position = 0.117 rotated from previous position = 0.16 degrees atoms outside contour = 2458, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51209517 0.38871214 -0.76593825 210.05378869 -0.64558628 0.76237656 -0.04472500 151.92672471 0.56654823 0.51738268 0.64135658 123.73458620 Axis 0.31614733 -0.74943299 -0.58172250 Axis point 77.70509195 0.00000000 274.04117698 Rotation angle (degrees) 62.74740644 Shift along axis -119.43014829 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 96 shifted from previous position = 0.0244 rotated from previous position = 0.0742 degrees atoms outside contour = 2460, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51252994 0.38857561 -0.76571669 210.03698454 -0.64470902 0.76314551 -0.04426304 151.89149117 0.56715371 0.51635059 0.64165312 123.73670817 Axis 0.31544427 -0.74997522 -0.58140526 Axis point 77.64642931 -0.00000000 274.14074650 Rotation angle (degrees) 62.69905013 Shift along axis -119.60106530 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 44 shifted from previous position = 0.0281 rotated from previous position = 0.029 degrees atoms outside contour = 2461, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51242156 0.38882713 -0.76566155 210.01796870 -0.64460272 0.76326236 -0.04379379 151.86034557 0.56737243 0.51598840 0.64175112 123.74083617 Axis 0.31498618 -0.75009046 -0.58150496 Axis point 77.66342323 0.00000000 274.08798434 Rotation angle (degrees) 62.69561739 Shift along axis -119.71214829 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 100 shifted from previous position = 0.0466 rotated from previous position = 0.0644 degrees atoms outside contour = 2462, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51166602 0.38840812 -0.76637916 210.07158022 -0.64471545 0.76317515 -0.04365407 151.86172524 0.56792593 0.51643279 0.64090351 123.79455855 Axis 0.31500312 -0.75043765 -0.58104764 Axis point 77.65472096 0.00000000 273.83618198 Rotation angle (degrees) 62.75010172 Shift along axis -119.72008940 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00553, steps = 96 shifted from previous position = 0.0996 rotated from previous position = 0.138 degrees atoms outside contour = 2458, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51090883 0.38729468 -0.76744706 210.17500163 -0.64551891 0.76241854 -0.04498117 151.97224586 0.56769490 0.51838287 0.63953240 123.85073800 Axis 0.31658224 -0.75028260 -0.58038927 Axis point 77.62049672 0.00000000 273.63540607 Rotation angle (degrees) 62.84302635 Shift along axis -119.36609759 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 64 shifted from previous position = 0.0703 rotated from previous position = 0.0889 degrees atoms outside contour = 2459, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51062337 0.38789634 -0.76733318 210.16606925 -0.64505183 0.76289402 -0.04359872 151.86550028 0.56848211 0.51723220 0.63976476 123.85255643 Axis 0.31519714 -0.75075241 -0.58053560 Axis point 77.66448784 0.00000000 273.51700457 Rotation angle (degrees) 62.82942632 Shift along axis -119.67046351 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 116 shifted from previous position = 0.091 rotated from previous position = 0.13 degrees atoms outside contour = 2463, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51236517 0.38829156 -0.76597101 210.04332404 -0.64442226 0.76339869 -0.04407250 151.88716540 0.56762829 0.51618998 0.64136263 123.76290188 Axis 0.31522819 -0.75034133 -0.58104998 Axis point 77.61522185 -0.00000000 274.05500256 Rotation angle (degrees) 62.70556477 Shift along axis -119.66807266 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005529, steps = 112 shifted from previous position = 0.112 rotated from previous position = 0.21 degrees atoms outside contour = 2459, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.50921426 0.38911465 -0.76765267 210.15109864 -0.64586593 0.76229301 -0.04203042 151.76564062 0.56882161 0.51720320 0.63948637 123.86975591 Axis 0.31409240 -0.75062802 -0.58129471 Axis point 77.84203569 0.00000000 273.05645537 Rotation angle (degrees) 62.90309475 Shift along axis -119.91751231 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00553, steps = 80 shifted from previous position = 0.134 rotated from previous position = 0.152 degrees atoms outside contour = 2458, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51000628 0.38728016 -0.76805447 210.20173705 -0.64585972 0.76215455 -0.04456087 151.95399423 0.56811867 0.51878177 0.63883226 123.89869822 Axis 0.31640018 -0.75045876 -0.58026078 Axis point 77.65380353 0.00000000 273.33562913 Rotation angle (degrees) 62.90311288 Shift along axis -119.42089464 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00553, steps = 60 shifted from previous position = 0.048 rotated from previous position = 0.0742 degrees atoms outside contour = 2458, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51085219 0.38777489 -0.76724225 210.15448160 -0.64562059 0.76235675 -0.04456726 151.93791122 0.56763024 0.51811468 0.63980706 123.83562452 Axis 0.31621318 -0.75016496 -0.58074242 Axis point 77.66568818 0.00000000 273.62081377 Rotation angle (degrees) 62.83799640 Shift along axis -119.44148097 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005532, steps = 60 shifted from previous position = 0.0803 rotated from previous position = 0.136 degrees atoms outside contour = 2462, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51131368 0.38839600 -0.76662042 210.09204897 -0.64447476 0.76341126 -0.04307592 151.82293746 0.56851615 0.51609281 0.64065404 123.81592876 Axis 0.31445345 -0.75082578 -0.58084394 Axis point 77.65907392 0.00000000 273.70410117 Rotation angle (degrees) 62.76188533 Shift along axis -119.84613728 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 48 shifted from previous position = 0.0949 rotated from previous position = 0.138 degrees atoms outside contour = 2457, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.50980264 0.38765872 -0.76799869 210.22522042 -0.64529487 0.76270172 -0.04336604 151.85199767 0.56894270 0.51769374 0.63898153 123.90053003 Axis 0.31516266 -0.75099664 -0.58023836 Axis point 77.67704017 0.00000000 273.26332412 Rotation angle (degrees) 62.88725307 Shift along axis -119.67703950 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 80 shifted from previous position = 0.191 rotated from previous position = 0.278 degrees atoms outside contour = 2462, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51331778 0.38894500 -0.76500108 209.97061280 -0.64413665 0.76364611 -0.04396132 151.86290174 0.56709156 0.51533136 0.64252685 123.69783906 Axis 0.31489904 -0.75000927 -0.58165685 Axis point 77.62890670 0.00000000 274.36885181 Rotation angle (degrees) 62.62932226 Shift along axis -119.72873536 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 88 shifted from previous position = 0.0975 rotated from previous position = 0.184 degrees atoms outside contour = 2459, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51075535 0.38875633 -0.76680994 210.11053718 -0.64534329 0.76267067 -0.04319125 151.83183731 0.56803258 0.51691582 0.64041941 123.81191141 Axis 0.31484151 -0.75032767 -0.58127723 Axis point 77.74310762 -0.00000000 273.56794804 Rotation angle (degrees) 62.81128651 Shift along axis -119.74115466 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00553, steps = 104 shifted from previous position = 0.028 rotated from previous position = 0.0301 degrees atoms outside contour = 2459, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51098033 0.38832899 -0.76687658 210.11986306 -0.64521466 0.76275195 -0.04367496 151.86884889 0.56797636 0.51711706 0.64030680 123.81685063 Axis 0.31524416 -0.75037549 -0.58099720 Axis point 77.69532411 0.00000000 273.63782877 Rotation angle (degrees) 62.80504918 Shift along axis -119.65684626 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00553, steps = 44 shifted from previous position = 0.0467 rotated from previous position = 0.0602 degrees atoms outside contour = 2459, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51143337 0.38895347 -0.76625785 210.07316381 -0.64509218 0.76287546 -0.04332563 151.83368864 0.56770766 0.51646512 0.64107081 123.77052693 Axis 0.31480331 -0.75016737 -0.58150477 Axis point 77.73327714 0.00000000 273.78575954 Rotation angle (degrees) 62.76186370 Shift along axis -119.74210396 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 48 shifted from previous position = 0.0329 rotated from previous position = 0.0469 degrees atoms outside contour = 2462, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51155389 0.38855821 -0.76637793 210.05995836 -0.64450539 0.76338031 -0.04316610 151.83246163 0.56826527 0.51601649 0.64093803 123.79575372 Axis 0.31450617 -0.75065555 -0.58103538 Axis point 77.66788891 0.00000000 273.77263954 Rotation angle (degrees) 62.74599140 Shift along axis -119.83844052 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 84 shifted from previous position = 0.102 rotated from previous position = 0.159 degrees atoms outside contour = 2459, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.50991642 0.38760799 -0.76794875 210.19393625 -0.64543566 0.76256481 -0.04367743 151.88740595 0.56868097 0.51793335 0.63902034 123.89975679 Axis 0.31547359 -0.75082495 -0.58029156 Axis point 77.67033136 0.00000000 273.28453780 Rotation angle (degrees) 62.88674883 Shift along axis -119.62820169 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.005531, steps = 64 shifted from previous position = 0.0568 rotated from previous position = 0.0708 degrees atoms outside contour = 2460, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51078090 0.38791869 -0.76721702 210.13288473 -0.64547235 0.76250406 -0.04419268 151.91555114 0.56786293 0.51779015 0.63986330 123.84325854 Axis 0.31583235 -0.75031016 -0.58076207 Axis point 77.66892880 0.00000000 273.57384931 Rotation angle (degrees) 62.83373735 Shift along axis -119.54048779 > fitmap #1 inMap #2 Fit molecule hnRNPA1A_joined_1.pdb (#1) to map postprocess_masked_job250.mrc (#2) using 2736 atoms average map value = 0.00553, steps = 60 shifted from previous position = 0.0755 rotated from previous position = 0.0807 degrees atoms outside contour = 2458, contour level = 0.021834 Position of hnRNPA1A_joined_1.pdb (#1) relative to postprocess_masked_job250.mrc (#2) coordinates: Matrix rotation and translation 0.51007010 0.38710270 -0.76810155 210.22655094 -0.64550442 0.76246514 -0.04439542 151.93571244 0.56846507 0.51845772 0.63878718 123.90136177 Axis 0.31615518 -0.75075083 -0.58001647 Axis point 77.63000684 0.00000000 273.35348524 Rotation angle (degrees) 62.89251426 Shift along axis -119.46647881 > save /data/lukas/hnRNPA1A/hnRNPA1m/isolde/hnRNAPA1_10.cxs includeMaps true ——— End of log from Tue Jun 11 01:13:06 2024 ——— opened ChimeraX session > select subtract #1 Nothing selected > hide #!2 models > select #1:293-349 728 atoms, 740 bonds, 57 residues, 1 model selected > show #!2 models > select up 1173 atoms, 1195 bonds, 124 residues, 1 model selected > select down 728 atoms, 740 bonds, 57 residues, 1 model selected > clipper associate #2 toModel #1 Opened postprocess_masked_job250.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.3, shown at level 0.00928, step 1, values float32 > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 46 residues in model #1.2 to IUPAC-IUB standards. > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > select #1:293-349 728 atoms, 740 bonds, 57 residues, 1 model selected > isolde sim start /A:293-349 Sim termination reason: None ISOLDE: stopped sim > addh Summary of feedback from adding hydrogens to hnRNPA1A_joined_1.pdb #1.2 --- notes | No usable SEQRES records for hnRNPA1A_joined_1.pdb (#1.2) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A PHE 669 Chain-final residues that are not actual C termini: 196 hydrogen bonds 1919 hydrogens added > isolde sim start /A:238-647 ISOLDE: started sim > ui tool show "Ramachandran Plot" > isolde sim stop > set selectionWidth 4 No simulation is currently running! > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > isolde sim stop > set selectionWidth 4 No simulation is currently running! > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > isolde sim pause > set selectionWidth 4 No simulation is currently running! > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > clipper spotlight > ui mousemode right "isolde tug selection" > select up 4655 atoms, 4707 bonds, 320 residues, 3 models selected > select add #1.2 4655 atoms, 4707 bonds, 320 residues, 14 models selected > select add #1.2 4655 atoms, 4707 bonds, 320 residues, 14 models selected > select add #1.2 4655 atoms, 4707 bonds, 320 residues, 14 models selected > isolde sim stop > set selectionWidth 4 No simulation is currently running! > isolde set simFidelityMode Highest/Slowest ISOLDE: setting sim fidelity mode to Highest/Slowest nonbonded_cutoff_distance = 1.700000 use_gbsa = True gbsa_cutoff = 2.000000 > select #1:1-249 3606 atoms, 3641 bonds, 240 residues, 1 model selected > isolde sim pause No simulation is currently running! > isolde sim start /A ISOLDE: started sim Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 909, in _dihe_r_changed_cb self.sim_handler.update_dihedral_restraints(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1816, in update_dihedral_restraints force.update_targets(restraints.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in update_targets _openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in update_targets _openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this), indices, params) See log for complete Python traceback. > volume #1.1.1.1 level 0.008823 > select #1:1-249 3606 atoms, 3641 bonds, 240 residues, 1 model selected > select #1:1-200 3134 atoms, 3163 bonds, 200 residues, 1 model selected > ui mousemode right "isolde tug selection" Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range [*many* of these deleted to fit within ticket limits] Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. Traceback (most recent call last): File "/usr/local/chimerax-1.6.1/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 978, in _tug_changed_cb self.sim_handler.update_tuggables(all_changeds) File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 2301, in update_tuggables force.update_targets(tuggables.sim_indices, File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range Error processing trigger "changes": RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of range File "/usr/users/lukas/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/custom_forces.py", line 1156, in update_targets _openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this), indices, params) See log for complete Python traceback. > ui mousemode right "translate selected models" > view matrix models #1.2,1,0,0,26.615,0,1,0,6.4844,0,0,1,-30.754 > view matrix models #1.2,1,0,0,0.60523,0,1,0,-1.8756,0,0,1,0.6088 > undo [Repeated 1 time(s)] OpenGL version: 3.3.0 NVIDIA 510.108.03 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_IE.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:0 Manufacturer: HP Model: HP Z1 Entry Tower G5 OS: Ubuntu 20.04 Focal Fossa Architecture: 64bit ELF Virtual Machine: none CPU: 16 Intel(R) Core(TM) i9-9900 CPU @ 3.10GHz Cache Size: 16384 KB Memory: total used free shared buff/cache available Mem: 62Gi 15Gi 9.5Gi 1.0Gi 37Gi 45Gi Swap: 55Gi 4.8Gi 51Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop 9 Series) [8086:3e98] (rev 02) DeviceName: Onboard IGD Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop 9 Series) [103c:8591] Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0
Change History (1)
comment:1 by , 17 months ago
Component: | Unassigned → Third Party |
---|---|
Description: | modified (diff) |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → ISOLDE tug: Assertion failure at CustomExternalForce.cpp:104. Index out of range |
Note:
See TracTickets
for help on using tickets.