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Opened 17 months ago

Last modified 17 months ago

#15403 assigned defect

ChimeraX bug report submission — at Initial Version

Reported by:	chimerax-bug-report@…	Owned by:
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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  
  
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  
  
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  
  
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  
  
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.  
  

> 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

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