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Opened 23 hours ago
Closed 23 hours ago
#19381 closed defect (duplicate)
ffmpeg: Permission Denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/fionaoyatsi/Library/CloudStorage/OneDrive-
> UniversitätMünster/Alignment/Rationalization/Journals/Figures and Tables/Fig
> 1_Crytal Structures of protein Targets used to generate Dynophores/3MCV
> Images/3MCV_tetramer_2.pdb" format pdb
[Repeated 9 time(s)]
> open "/Users/fionaoyatsi/Library/CloudStorage/OneDrive-
> UniversitätMünster/Alignment/Rationalization/Crystal Structure
> Analysis/3MCV/3MCV_d/3MCV_MCV_1d_all.pdb"
Summary of feedback from opening
/Users/fionaoyatsi/Library/CloudStorage/OneDrive-
UniversitätMünster/Alignment/Rationalization/Crystal Structure
Analysis/3MCV/3MCV_d/3MCV_MCV_1d_all.pdb
---
warnings | Ignored bad PDB record found on line 46675
ATOM 46674 O T3P X271a 16.362 46.174 41.895 0.00 0.00 C6 O
Ignored bad PDB record found on line 46676
ATOM 46675 H1 T3P X271a 16.172 45.245 41.759 0.00 0.00 C6 H
Ignored bad PDB record found on line 46677
ATOM 46676 H2 T3P X271a 15.588 46.514 42.344 0.00 0.00 C6 H
Ignored bad PDB record found on line 46678
ATOM 46677 O T3P X271b -12.615 22.597 -49.858 0.00 0.00 C6 O
Ignored bad PDB record found on line 46679
ATOM 46678 H1 T3P X271b -11.693 22.762 -49.664 0.00 0.00 C6 H
43141 messages similar to the above omitted
Duplicate atom serial number found: 19104
Duplicate atom serial number found: 19105
Duplicate atom serial number found: 19106
Duplicate atom serial number found: 19107
Duplicate atom serial number found: 19108
1 messages similar to the above omitted
Ignored bad PDB record found on line 102667
ATOM 1910a O T3P X7002 31.881 29.504 -29.911 0.00 0.00 C6 O
Ignored bad PDB record found on line 102668
ATOM 1910b H1 T3P X7002 30.966 29.229 -29.973 0.00 0.00 C6 H
Ignored bad PDB record found on line 102669
ATOM 1910c H2 T3P X7002 32.020 29.667 -28.979 0.00 0.00 C6 H
Ignored bad PDB record found on line 102670
ATOM 1910d O T3P X7003 -18.082 -54.546 19.532 0.00 0.00 C6 O
Ignored bad PDB record found on line 102671
ATOM 1910e H1 T3P X7003 -18.841 -54.403 20.097 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19110
Duplicate atom serial number found: 19111
Duplicate atom serial number found: 19112
Duplicate atom serial number found: 19113
Duplicate atom serial number found: 19114
5 messages similar to the above omitted
Ignored bad PDB record found on line 102683
ATOM 1911a H1 T3P X7007 -35.781 32.953 -7.140 0.00 0.00 C6 H
Ignored bad PDB record found on line 102684
ATOM 1911b H2 T3P X7007 -35.326 32.764 -5.709 0.00 0.00 C6 H
Ignored bad PDB record found on line 102685
ATOM 1911c O T3P X7008 24.682 -27.772 19.580 0.00 0.00 C6 O
Ignored bad PDB record found on line 102686
ATOM 1911d H1 T3P X7008 25.014 -28.402 20.219 0.00 0.00 C6 H
Ignored bad PDB record found on line 102687
ATOM 1911e H2 T3P X7008 25.202 -27.932 18.793 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19120
Duplicate atom serial number found: 19121
Ignored bad PDB record found on line 102691
ATOM 19122 O T3P X700a 1.226 42.575 -18.377 0.00 0.00 C6 O
Ignored bad PDB record found on line 102692
ATOM 19123 H1 T3P X700a 0.639 42.656 -19.129 0.00 0.00 C6 H
Ignored bad PDB record found on line 102693
ATOM 19124 H2 T3P X700a 1.187 43.430 -17.949 0.00 0.00 C6 H
Ignored bad PDB record found on line 102694
ATOM 19125 O T3P X700b -30.817 13.803 44.273 0.00 0.00 C6 O
Ignored bad PDB record found on line 102695
ATOM 19126 H1 T3P X700b -30.368 13.948 43.440 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19134
Duplicate atom serial number found: 19135
Duplicate atom serial number found: 19136
Duplicate atom serial number found: 19137
Duplicate atom serial number found: 19138
1 messages similar to the above omitted
Ignored bad PDB record found on line 102715
ATOM 1913a O T3P X7012 -7.437 27.309 35.318 0.00 0.00 C6 O
Ignored bad PDB record found on line 102716
ATOM 1913b H1 T3P X7012 -7.493 27.095 34.386 0.00 0.00 C6 H
Ignored bad PDB record found on line 102717
ATOM 1913c H2 T3P X7012 -6.558 27.670 35.429 0.00 0.00 C6 H
Ignored bad PDB record found on line 102718
ATOM 1913d O T3P X7013 7.332 -50.378 45.425 0.00 0.00 C6 O
Ignored bad PDB record found on line 102719
ATOM 1913e H1 T3P X7013 7.970 -50.094 44.770 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19140
Duplicate atom serial number found: 19141
Duplicate atom serial number found: 19142
Duplicate atom serial number found: 19143
Duplicate atom serial number found: 19144
5 messages similar to the above omitted
Ignored bad PDB record found on line 102731
ATOM 1914a H1 T3P X7017 -31.110 -18.146 18.325 0.00 0.00 C6 H
Ignored bad PDB record found on line 102732
ATOM 1914b H2 T3P X7017 -30.449 -18.108 19.687 0.00 0.00 C6 H
Ignored bad PDB record found on line 102733
ATOM 1914c O T3P X7018 24.013 43.921 -49.444 0.00 0.00 C6 O
Ignored bad PDB record found on line 102734
ATOM 1914d H1 T3P X7018 24.580 43.529 -48.779 0.00 0.00 C6 H
Ignored bad PDB record found on line 102735
ATOM 1914e H2 T3P X7018 24.534 44.633 -49.815 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19150
Duplicate atom serial number found: 19151
Ignored bad PDB record found on line 102739
ATOM 19152 O T3P X701a -21.922 41.528 23.043 0.00 0.00 C6 O
Ignored bad PDB record found on line 102740
ATOM 19153 H1 T3P X701a -21.355 41.449 22.276 0.00 0.00 C6 H
Ignored bad PDB record found on line 102741
ATOM 19154 H2 T3P X701a -21.901 42.459 23.262 0.00 0.00 C6 H
Ignored bad PDB record found on line 102742
ATOM 19155 O T3P X701b 36.060 -29.317 34.099 0.00 0.00 C6 O
Ignored bad PDB record found on line 102743
ATOM 19156 H1 T3P X701b 35.755 -29.647 33.254 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19164
Duplicate atom serial number found: 19165
Duplicate atom serial number found: 19166
Duplicate atom serial number found: 19167
Duplicate atom serial number found: 19168
1 messages similar to the above omitted
Ignored bad PDB record found on line 102763
ATOM 1916a O T3P X7022 28.382 39.329 10.900 0.00 0.00 C6 O
Ignored bad PDB record found on line 102764
ATOM 1916b H1 T3P X7022 27.931 38.486 10.945 0.00 0.00 C6 H
Ignored bad PDB record found on line 102765
ATOM 1916c H2 T3P X7022 29.230 39.126 10.506 0.00 0.00 C6 H
Ignored bad PDB record found on line 102766
ATOM 1916d O T3P X7023 2.750 -44.827 -21.186 0.00 0.00 C6 O
Ignored bad PDB record found on line 102767
ATOM 1916e H1 T3P X7023 2.085 -44.922 -21.867 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19170
Duplicate atom serial number found: 19171
Duplicate atom serial number found: 19172
Duplicate atom serial number found: 19173
Duplicate atom serial number found: 19174
5 messages similar to the above omitted
Ignored bad PDB record found on line 102779
ATOM 1917a H1 T3P X7027 25.367 -44.101 33.570 0.00 0.00 C6 H
Ignored bad PDB record found on line 102780
ATOM 1917b H2 T3P X7027 26.413 -45.173 33.786 0.00 0.00 C6 H
Ignored bad PDB record found on line 102781
ATOM 1917c O T3P X7028 28.460 -36.276 38.266 0.00 0.00 C6 O
Ignored bad PDB record found on line 102782
ATOM 1917d H1 T3P X7028 28.180 -37.132 38.590 0.00 0.00 C6 H
Ignored bad PDB record found on line 102783
ATOM 1917e H2 T3P X7028 28.498 -35.723 39.046 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19180
Duplicate atom serial number found: 19181
Ignored bad PDB record found on line 102787
ATOM 19182 O T3P X702a -35.903 41.323 33.085 0.00 0.00 C6 O
Ignored bad PDB record found on line 102788
ATOM 19183 H1 T3P X702a -36.824 41.301 32.823 0.00 0.00 C6 H
Ignored bad PDB record found on line 102789
ATOM 19184 H2 T3P X702a -35.579 40.443 32.898 0.00 0.00 C6 H
Ignored bad PDB record found on line 102790
ATOM 19185 O T3P X702b 17.381 -18.778 -40.331 0.00 0.00 C6 O
Ignored bad PDB record found on line 102791
ATOM 19186 H1 T3P X702b 17.759 -18.180 -40.976 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19194
Duplicate atom serial number found: 19195
Duplicate atom serial number found: 19196
Duplicate atom serial number found: 19197
Duplicate atom serial number found: 19198
1 messages similar to the above omitted
Ignored bad PDB record found on line 102811
ATOM 1919a O T3P X7032 -42.482 8.439 -41.156 0.00 0.00 C6 O
Ignored bad PDB record found on line 102812
ATOM 1919b H1 T3P X7032 -42.483 7.517 -41.414 0.00 0.00 C6 H
Ignored bad PDB record found on line 102813
ATOM 1919c H2 T3P X7032 -43.383 8.612 -40.881 0.00 0.00 C6 H
Ignored bad PDB record found on line 102814
ATOM 1919d O T3P X7033 47.983 23.304 31.865 0.00 0.00 C6 O
Ignored bad PDB record found on line 102815
ATOM 1919e H1 T3P X7033 48.510 22.506 31.841 0.00 0.00 C6 H
97 messages similar to the above omitted
Duplicate atom serial number found: 19200
Duplicate atom serial number found: 19201
Duplicate atom serial number found: 19202
Duplicate atom serial number found: 19203
Duplicate atom serial number found: 19204
5 messages similar to the above omitted
Ignored bad PDB record found on line 102923
ATOM 1920a H1 T3P X7057 10.474 42.731 -39.895 0.00 0.00 C6 H
Ignored bad PDB record found on line 102924
ATOM 1920b H2 T3P X7057 9.810 41.745 -38.958 0.00 0.00 C6 H
Ignored bad PDB record found on line 102925
ATOM 1920c O T3P X7058 31.323 53.115 14.977 0.00 0.00 C6 O
Ignored bad PDB record found on line 102926
ATOM 1920d H1 T3P X7058 30.701 52.656 15.542 0.00 0.00 C6 H
Ignored bad PDB record found on line 102927
ATOM 1920e H2 T3P X7058 30.886 53.938 14.758 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19210
Duplicate atom serial number found: 19211
Ignored bad PDB record found on line 102931
ATOM 19212 O T3P X705a -22.712 -44.345 -17.204 0.00 0.00 C6 O
Ignored bad PDB record found on line 102932
ATOM 19213 H1 T3P X705a -21.918 -44.727 -16.832 0.00 0.00 C6 H
Ignored bad PDB record found on line 102933
ATOM 19214 H2 T3P X705a -22.877 -43.567 -16.672 0.00 0.00 C6 H
Ignored bad PDB record found on line 102934
ATOM 19215 O T3P X705b -45.245 -36.752 24.384 0.00 0.00 C6 O
Ignored bad PDB record found on line 102935
ATOM 19216 H1 T3P X705b -45.928 -36.616 23.727 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19224
Duplicate atom serial number found: 19225
Duplicate atom serial number found: 19226
Duplicate atom serial number found: 19227
Duplicate atom serial number found: 19228
1 messages similar to the above omitted
Ignored bad PDB record found on line 102955
ATOM 1922a O T3P X7062 34.889 47.253 36.632 0.00 0.00 C6 O
Ignored bad PDB record found on line 102956
ATOM 1922b H1 T3P X7062 34.060 47.728 36.692 0.00 0.00 C6 H
Ignored bad PDB record found on line 102957
ATOM 1922c H2 T3P X7062 34.667 46.439 36.180 0.00 0.00 C6 H
Ignored bad PDB record found on line 102958
ATOM 1922d O T3P X7063 5.795 -58.182 -5.263 0.00 0.00 C6 O
Ignored bad PDB record found on line 102959
ATOM 1922e H1 T3P X7063 6.663 -58.424 -5.586 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19230
Duplicate atom serial number found: 19231
Duplicate atom serial number found: 19232
Duplicate atom serial number found: 19233
Duplicate atom serial number found: 19234
5 messages similar to the above omitted
Ignored bad PDB record found on line 102971
ATOM 1923a H1 T3P X7067 -47.197 -55.810 23.899 0.00 0.00 C6 H
Ignored bad PDB record found on line 102972
ATOM 1923b H2 T3P X7067 -47.933 -54.617 23.328 0.00 0.00 C6 H
Ignored bad PDB record found on line 102973
ATOM 1923c O T3P X7068 13.427 -25.077 -33.381 0.00 0.00 C6 O
Ignored bad PDB record found on line 102974
ATOM 1923d H1 T3P X7068 14.206 -24.892 -33.906 0.00 0.00 C6 H
Ignored bad PDB record found on line 102975
ATOM 1923e H2 T3P X7068 13.317 -26.026 -33.440 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19240
Duplicate atom serial number found: 19241
Ignored bad PDB record found on line 102979
ATOM 19242 O T3P X706a -28.625 28.437 -50.326 0.00 0.00 C6 O
Ignored bad PDB record found on line 102980
ATOM 19243 H1 T3P X706a -28.879 29.301 -50.003 0.00 0.00 C6 H
Ignored bad PDB record found on line 102981
ATOM 19244 H2 T3P X706a -29.425 28.078 -50.708 0.00 0.00 C6 H
Ignored bad PDB record found on line 102982
ATOM 19245 O T3P X706b 7.466 -10.085 -51.528 0.00 0.00 C6 O
Ignored bad PDB record found on line 102983
ATOM 19246 H1 T3P X706b 8.013 -9.446 -51.070 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19254
Duplicate atom serial number found: 19255
Duplicate atom serial number found: 19256
Duplicate atom serial number found: 19257
Duplicate atom serial number found: 19258
1 messages similar to the above omitted
Ignored bad PDB record found on line 103003
ATOM 1925a O T3P X7072 -16.821 51.285 20.859 0.00 0.00 C6 O
Ignored bad PDB record found on line 103004
ATOM 1925b H1 T3P X7072 -16.012 51.043 20.407 0.00 0.00 C6 H
Ignored bad PDB record found on line 103005
ATOM 1925c H2 T3P X7072 -16.528 51.658 21.691 0.00 0.00 C6 H
Ignored bad PDB record found on line 103006
ATOM 1925d O T3P X7073 31.576 49.432 -43.310 0.00 0.00 C6 O
Ignored bad PDB record found on line 103007
ATOM 1925e H1 T3P X7073 30.700 49.432 -43.697 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19260
Duplicate atom serial number found: 19261
Duplicate atom serial number found: 19262
Duplicate atom serial number found: 19263
Duplicate atom serial number found: 19264
5 messages similar to the above omitted
Ignored bad PDB record found on line 103019
ATOM 1926a H1 T3P X7077 -2.656 -46.715 32.229 0.00 0.00 C6 H
Ignored bad PDB record found on line 103020
ATOM 1926b H2 T3P X7077 -2.423 -48.118 31.710 0.00 0.00 C6 H
Ignored bad PDB record found on line 103021
ATOM 1926c O T3P X7078 -4.218 -22.721 -32.824 0.00 0.00 C6 O
Ignored bad PDB record found on line 103022
ATOM 1926d H1 T3P X7078 -4.134 -23.673 -32.773 0.00 0.00 C6 H
Ignored bad PDB record found on line 103023
ATOM 1926e H2 T3P X7078 -5.159 -22.568 -32.914 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19270
Duplicate atom serial number found: 19271
Ignored bad PDB record found on line 103027
ATOM 19272 O T3P X707a 38.457 30.094 -42.089 0.00 0.00 C6 O
Ignored bad PDB record found on line 103028
ATOM 19273 H1 T3P X707a 37.709 29.976 -41.504 0.00 0.00 C6 H
Ignored bad PDB record found on line 103029
ATOM 19274 H2 T3P X707a 38.737 30.998 -41.941 0.00 0.00 C6 H
Ignored bad PDB record found on line 103030
ATOM 19275 O T3P X707b 4.345 25.888 -24.479 0.00 0.00 C6 O
Ignored bad PDB record found on line 103031
ATOM 19276 H1 T3P X707b 3.794 25.114 -24.368 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19284
Duplicate atom serial number found: 19285
Duplicate atom serial number found: 19286
Duplicate atom serial number found: 19287
Duplicate atom serial number found: 19288
1 messages similar to the above omitted
Ignored bad PDB record found on line 103051
ATOM 1928a O T3P X7082 -22.418 -16.924 -33.844 0.00 0.00 C6 O
Ignored bad PDB record found on line 103052
ATOM 1928b H1 T3P X7082 -21.847 -16.882 -34.611 0.00 0.00 C6 H
Ignored bad PDB record found on line 103053
ATOM 1928c H2 T3P X7082 -22.600 -16.010 -33.630 0.00 0.00 C6 H
Ignored bad PDB record found on line 103054
ATOM 1928d O T3P X7083 15.461 -44.188 -13.612 0.00 0.00 C6 O
Ignored bad PDB record found on line 103055
ATOM 1928e H1 T3P X7083 15.861 -45.027 -13.842 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19290
Duplicate atom serial number found: 19291
Duplicate atom serial number found: 19292
Duplicate atom serial number found: 19293
Duplicate atom serial number found: 19294
5 messages similar to the above omitted
Ignored bad PDB record found on line 103067
ATOM 1929a H1 T3P X7087 23.954 -4.749 -29.008 0.00 0.00 C6 H
Ignored bad PDB record found on line 103068
ATOM 1929b H2 T3P X7087 24.385 -6.199 -28.947 0.00 0.00 C6 H
Ignored bad PDB record found on line 103069
ATOM 1929c O T3P X7088 13.373 -21.448 31.955 0.00 0.00 C6 O
Ignored bad PDB record found on line 103070
ATOM 1929d H1 T3P X7088 13.276 -20.707 31.357 0.00 0.00 C6 H
Ignored bad PDB record found on line 103071
ATOM 1929e H2 T3P X7088 13.937 -21.120 32.655 0.00 0.00 C6 H
357 messages similar to the above omitted
Duplicate atom serial number found: 19404
Duplicate atom serial number found: 19405
Duplicate atom serial number found: 19406
Duplicate atom serial number found: 19407
Duplicate atom serial number found: 19408
1 messages similar to the above omitted
Ignored bad PDB record found on line 103435
ATOM 1940a O T3P X7102 41.687 34.018 -16.785 0.00 0.00 C6 O
Ignored bad PDB record found on line 103436
ATOM 1940b H1 T3P X7102 41.849 34.176 -17.715 0.00 0.00 C6 H
Ignored bad PDB record found on line 103437
ATOM 1940c H2 T3P X7102 40.868 33.523 -16.764 0.00 0.00 C6 H
Ignored bad PDB record found on line 103438
ATOM 1940d O T3P X7103 -17.697 57.138 -50.587 0.00 0.00 C6 O
Ignored bad PDB record found on line 103439
ATOM 1940e H1 T3P X7103 -18.132 57.057 -51.436 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19410
Duplicate atom serial number found: 19411
Duplicate atom serial number found: 19412
Duplicate atom serial number found: 19413
Duplicate atom serial number found: 19414
5 messages similar to the above omitted
Ignored bad PDB record found on line 103451
ATOM 1941a H1 T3P X7107 -3.269 35.724 -37.769 0.00 0.00 C6 H
Ignored bad PDB record found on line 103452
ATOM 1941b H2 T3P X7107 -3.268 35.117 -36.382 0.00 0.00 C6 H
Ignored bad PDB record found on line 103453
ATOM 1941c O T3P X7108 -41.451 22.580 47.943 0.00 0.00 C6 O
Ignored bad PDB record found on line 103454
ATOM 1941d H1 T3P X7108 -41.149 23.461 48.164 0.00 0.00 C6 H
Ignored bad PDB record found on line 103455
ATOM 1941e H2 T3P X7108 -40.923 22.000 48.490 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19420
Duplicate atom serial number found: 19421
Ignored bad PDB record found on line 103459
ATOM 19422 O T3P X710a -30.525 -36.827 16.447 0.00 0.00 C6 O
Ignored bad PDB record found on line 103460
ATOM 19423 H1 T3P X710a -30.847 -36.434 17.259 0.00 0.00 C6 H
Ignored bad PDB record found on line 103461
ATOM 19424 H2 T3P X710a -30.159 -36.092 15.955 0.00 0.00 C6 H
Ignored bad PDB record found on line 103462
ATOM 19425 O T3P X710b 35.244 -30.562 -34.487 0.00 0.00 C6 O
Ignored bad PDB record found on line 103463
ATOM 19426 H1 T3P X710b 34.997 -29.642 -34.387 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19434
Duplicate atom serial number found: 19435
Duplicate atom serial number found: 19436
Duplicate atom serial number found: 19437
Duplicate atom serial number found: 19438
1 messages similar to the above omitted
Ignored bad PDB record found on line 103483
ATOM 1943a O T3P X7112 44.924 46.707 -23.667 0.00 0.00 C6 O
Ignored bad PDB record found on line 103484
ATOM 1943b H1 T3P X7112 44.562 47.586 -23.558 0.00 0.00 C6 H
Ignored bad PDB record found on line 103485
ATOM 1943c H2 T3P X7112 45.668 46.826 -24.258 0.00 0.00 C6 H
Ignored bad PDB record found on line 103486
ATOM 1943d O T3P X7113 42.341 -25.935 10.538 0.00 0.00 C6 O
Ignored bad PDB record found on line 103487
ATOM 1943e H1 T3P X7113 41.848 -25.676 11.316 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19440
Duplicate atom serial number found: 19441
Duplicate atom serial number found: 19442
Duplicate atom serial number found: 19443
Duplicate atom serial number found: 19444
5 messages similar to the above omitted
Ignored bad PDB record found on line 103499
ATOM 1944a H1 T3P X7117 8.688 -35.473 -52.222 0.00 0.00 C6 H
Ignored bad PDB record found on line 103500
ATOM 1944b H2 T3P X7117 8.847 -36.974 -52.338 0.00 0.00 C6 H
Ignored bad PDB record found on line 103501
ATOM 1944c O T3P X7118 9.300 35.348 -7.534 0.00 0.00 C6 O
Ignored bad PDB record found on line 103502
ATOM 1944d H1 T3P X7118 8.996 36.101 -8.041 0.00 0.00 C6 H
Ignored bad PDB record found on line 103503
ATOM 1944e H2 T3P X7118 8.661 35.262 -6.826 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19450
Duplicate atom serial number found: 19451
Ignored bad PDB record found on line 103507
ATOM 19452 O T3P X711a 47.089 -23.502 -23.418 0.00 0.00 C6 O
Ignored bad PDB record found on line 103508
ATOM 19453 H1 T3P X711a 46.526 -23.946 -22.785 0.00 0.00 C6 H
Ignored bad PDB record found on line 103509
ATOM 19454 H2 T3P X711a 47.959 -23.520 -23.019 0.00 0.00 C6 H
Ignored bad PDB record found on line 103510
ATOM 19455 O T3P X711b 14.202 -19.564 -0.923 0.00 0.00 C6 O
Ignored bad PDB record found on line 103511
ATOM 19456 H1 T3P X711b 13.472 -18.947 -0.975 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19464
Duplicate atom serial number found: 19465
Duplicate atom serial number found: 19466
Duplicate atom serial number found: 19467
Duplicate atom serial number found: 19468
1 messages similar to the above omitted
Ignored bad PDB record found on line 103531
ATOM 1946a O T3P X7122 31.349 -16.564 -4.943 0.00 0.00 C6 O
Ignored bad PDB record found on line 103532
ATOM 1946b H1 T3P X7122 30.979 -15.725 -4.669 0.00 0.00 C6 H
Ignored bad PDB record found on line 103533
ATOM 1946c H2 T3P X7122 30.744 -17.219 -4.595 0.00 0.00 C6 H
Ignored bad PDB record found on line 103534
ATOM 1946d O T3P X7123 -12.082 15.102 -48.070 0.00 0.00 C6 O
Ignored bad PDB record found on line 103535
ATOM 1946e H1 T3P X7123 -11.728 15.005 -47.186 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19470
Duplicate atom serial number found: 19471
Duplicate atom serial number found: 19472
Duplicate atom serial number found: 19473
Duplicate atom serial number found: 19474
5 messages similar to the above omitted
Ignored bad PDB record found on line 103547
ATOM 1947a H1 T3P X7127 35.113 -17.602 -29.437 0.00 0.00 C6 H
Ignored bad PDB record found on line 103548
ATOM 1947b H2 T3P X7127 34.844 -18.030 -28.010 0.00 0.00 C6 H
Ignored bad PDB record found on line 103549
ATOM 1947c O T3P X7128 -45.241 -25.698 28.114 0.00 0.00 C6 O
Ignored bad PDB record found on line 103550
ATOM 1947d H1 T3P X7128 -44.634 -25.577 27.384 0.00 0.00 C6 H
Ignored bad PDB record found on line 103551
ATOM 1947e H2 T3P X7128 -44.679 -25.740 28.888 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19480
Duplicate atom serial number found: 19481
Ignored bad PDB record found on line 103555
ATOM 19482 O T3P X712a -21.916 5.631 -17.054 0.00 0.00 C6 O
Ignored bad PDB record found on line 103556
ATOM 19483 H1 T3P X712a -22.051 6.542 -16.791 0.00 0.00 C6 H
Ignored bad PDB record found on line 103557
ATOM 19484 H2 T3P X712a -21.272 5.678 -17.760 0.00 0.00 C6 H
Ignored bad PDB record found on line 103558
ATOM 19485 O T3P X712b 23.065 -29.758 -11.915 0.00 0.00 C6 O
Ignored bad PDB record found on line 103559
ATOM 19486 H1 T3P X712b 22.971 -29.070 -12.574 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19494
Duplicate atom serial number found: 19495
Duplicate atom serial number found: 19496
Duplicate atom serial number found: 19497
Duplicate atom serial number found: 19498
1 messages similar to the above omitted
Ignored bad PDB record found on line 103579
ATOM 1949a O T3P X7132 37.902 11.485 6.683 0.00 0.00 C6 O
Ignored bad PDB record found on line 103580
ATOM 1949b H1 T3P X7132 37.457 10.866 6.104 0.00 0.00 C6 H
Ignored bad PDB record found on line 103581
ATOM 1949c H2 T3P X7132 37.358 11.509 7.471 0.00 0.00 C6 H
Ignored bad PDB record found on line 103582
ATOM 1949d O T3P X7133 -19.170 -35.267 -8.044 0.00 0.00 C6 O
Ignored bad PDB record found on line 103583
ATOM 1949e H1 T3P X7133 -19.599 -34.993 -8.854 0.00 0.00 C6 H
97 messages similar to the above omitted
Duplicate atom serial number found: 19500
Duplicate atom serial number found: 19501
Duplicate atom serial number found: 19502
Duplicate atom serial number found: 19503
Duplicate atom serial number found: 19504
5 messages similar to the above omitted
Ignored bad PDB record found on line 103691
ATOM 1950a H1 T3P X7157 1.007 19.646 -44.984 0.00 0.00 C6 H
Ignored bad PDB record found on line 103692
ATOM 1950b H2 T3P X7157 0.966 20.270 -46.363 0.00 0.00 C6 H
Ignored bad PDB record found on line 103693
ATOM 1950c O T3P X7158 44.142 3.553 29.313 0.00 0.00 C6 O
Ignored bad PDB record found on line 103694
ATOM 1950d H1 T3P X7158 44.760 3.176 29.939 0.00 0.00 C6 H
Ignored bad PDB record found on line 103695
ATOM 1950e H2 T3P X7158 43.494 4.002 29.856 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19510
Duplicate atom serial number found: 19511
Ignored bad PDB record found on line 103699
ATOM 19512 O T3P X715a -9.418 -36.162 6.958 0.00 0.00 C6 O
Ignored bad PDB record found on line 103700
ATOM 19513 H1 T3P X715a -10.355 -36.168 6.765 0.00 0.00 C6 H
Ignored bad PDB record found on line 103701
ATOM 19514 H2 T3P X715a -9.015 -36.598 6.207 0.00 0.00 C6 H
Ignored bad PDB record found on line 103702
ATOM 19515 O T3P X715b 32.269 37.948 -39.348 0.00 0.00 C6 O
Ignored bad PDB record found on line 103703
ATOM 19516 H1 T3P X715b 31.487 38.491 -39.248 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19524
Duplicate atom serial number found: 19525
Duplicate atom serial number found: 19526
Duplicate atom serial number found: 19527
Duplicate atom serial number found: 19528
1 messages similar to the above omitted
Ignored bad PDB record found on line 103723
ATOM 1952a O T3P X7162 2.167 36.257 29.561 0.00 0.00 C6 O
Ignored bad PDB record found on line 103724
ATOM 1952b H1 T3P X7162 2.475 36.899 30.200 0.00 0.00 C6 H
Ignored bad PDB record found on line 103725
ATOM 1952c H2 T3P X7162 2.458 36.600 28.716 0.00 0.00 C6 H
Ignored bad PDB record found on line 103726
ATOM 1952d O T3P X7163 -0.088 -53.394 4.176 0.00 0.00 C6 O
Ignored bad PDB record found on line 103727
ATOM 1952e H1 T3P X7163 -0.370 -53.676 3.306 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19530
Duplicate atom serial number found: 19531
Duplicate atom serial number found: 19532
Duplicate atom serial number found: 19533
Duplicate atom serial number found: 19534
5 messages similar to the above omitted
Ignored bad PDB record found on line 103739
ATOM 1953a H1 T3P X7167 42.434 -31.272 -6.133 0.00 0.00 C6 H
Ignored bad PDB record found on line 103740
ATOM 1953b H2 T3P X7167 43.674 -32.137 -6.071 0.00 0.00 C6 H
Ignored bad PDB record found on line 103741
ATOM 1953c O T3P X7168 9.545 52.060 27.564 0.00 0.00 C6 O
Ignored bad PDB record found on line 103742
ATOM 1953d H1 T3P X7168 9.351 52.996 27.527 0.00 0.00 C6 H
Ignored bad PDB record found on line 103743
ATOM 1953e H2 T3P X7168 9.603 51.791 26.647 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19540
Duplicate atom serial number found: 19541
Ignored bad PDB record found on line 103747
ATOM 19542 O T3P X716a -44.490 16.645 39.655 0.00 0.00 C6 O
Ignored bad PDB record found on line 103748
ATOM 19543 H1 T3P X716a -44.486 17.456 39.146 0.00 0.00 C6 H
Ignored bad PDB record found on line 103749
ATOM 19544 H2 T3P X716a -43.725 16.715 40.225 0.00 0.00 C6 H
Ignored bad PDB record found on line 103750
ATOM 19545 O T3P X716b 32.959 22.602 47.483 0.00 0.00 C6 O
Ignored bad PDB record found on line 103751
ATOM 19546 H1 T3P X716b 33.812 22.706 47.904 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19554
Duplicate atom serial number found: 19555
Duplicate atom serial number found: 19556
Duplicate atom serial number found: 19557
Duplicate atom serial number found: 19558
1 messages similar to the above omitted
Ignored bad PDB record found on line 103771
ATOM 1955a O T3P X7172 -18.752 34.127 9.006 0.00 0.00 C6 O
Ignored bad PDB record found on line 103772
ATOM 1955b H1 T3P X7172 -19.365 33.419 8.811 0.00 0.00 C6 H
Ignored bad PDB record found on line 103773
ATOM 1955c H2 T3P X7172 -19.202 34.921 8.717 0.00 0.00 C6 H
Ignored bad PDB record found on line 103774
ATOM 1955d O T3P X7173 48.393 -43.877 -42.136 0.00 0.00 C6 O
Ignored bad PDB record found on line 103775
ATOM 1955e H1 T3P X7173 47.545 -44.020 -42.558 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19560
Duplicate atom serial number found: 19561
Duplicate atom serial number found: 19562
Duplicate atom serial number found: 19563
Duplicate atom serial number found: 19564
5 messages similar to the above omitted
Ignored bad PDB record found on line 103787
ATOM 1956a H1 T3P X7177 38.294 -51.609 38.504 0.00 0.00 C6 H
Ignored bad PDB record found on line 103788
ATOM 1956b H2 T3P X7177 37.316 -51.232 39.596 0.00 0.00 C6 H
Ignored bad PDB record found on line 103789
ATOM 1956c O T3P X7178 -0.878 -9.889 36.638 0.00 0.00 C6 O
Ignored bad PDB record found on line 103790
ATOM 1956d H1 T3P X7178 -1.102 -10.819 36.619 0.00 0.00 C6 H
Ignored bad PDB record found on line 103791
ATOM 1956e H2 T3P X7178 -0.219 -9.787 35.951 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19570
Duplicate atom serial number found: 19571
Ignored bad PDB record found on line 103795
ATOM 19572 O T3P X717a -26.622 3.050 -42.461 0.00 0.00 C6 O
Ignored bad PDB record found on line 103796
ATOM 19573 H1 T3P X717a -25.761 2.698 -42.235 0.00 0.00 C6 H
Ignored bad PDB record found on line 103797
ATOM 19574 H2 T3P X717a -27.235 2.550 -41.921 0.00 0.00 C6 H
Ignored bad PDB record found on line 103798
ATOM 19575 O T3P X717b -46.593 -47.526 23.910 0.00 0.00 C6 O
Ignored bad PDB record found on line 103799
ATOM 19576 H1 T3P X717b -46.812 -47.800 24.801 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19584
Duplicate atom serial number found: 19585
Duplicate atom serial number found: 19586
Duplicate atom serial number found: 19587
Duplicate atom serial number found: 19588
1 messages similar to the above omitted
Ignored bad PDB record found on line 103819
ATOM 1958a O T3P X7182 -17.725 -51.789 -20.608 0.00 0.00 C6 O
Ignored bad PDB record found on line 103820
ATOM 1958b H1 T3P X7182 -18.246 -52.582 -20.482 0.00 0.00 C6 H
Ignored bad PDB record found on line 103821
ATOM 1958c H2 T3P X7182 -18.225 -51.102 -20.167 0.00 0.00 C6 H
Ignored bad PDB record found on line 103822
ATOM 1958d O T3P X7183 30.209 35.422 -6.179 0.00 0.00 C6 O
Ignored bad PDB record found on line 103823
ATOM 1958e H1 T3P X7183 29.396 35.138 -6.598 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19590
Duplicate atom serial number found: 19591
Duplicate atom serial number found: 19592
Duplicate atom serial number found: 19593
Duplicate atom serial number found: 19594
5 messages similar to the above omitted
Ignored bad PDB record found on line 103835
ATOM 1959a H1 T3P X7187 10.174 -26.660 40.151 0.00 0.00 C6 H
Ignored bad PDB record found on line 103836
ATOM 1959b H2 T3P X7187 10.440 -25.278 40.707 0.00 0.00 C6 H
Ignored bad PDB record found on line 103837
ATOM 1959c O T3P X7188 -38.709 0.743 19.986 0.00 0.00 C6 O
Ignored bad PDB record found on line 103838
ATOM 1959d H1 T3P X7188 -38.929 -0.178 20.123 0.00 0.00 C6 H
Ignored bad PDB record found on line 103839
ATOM 1959e H2 T3P X7188 -39.506 1.218 20.223 0.00 0.00 C6 H
357 messages similar to the above omitted
Duplicate atom serial number found: 19704
Duplicate atom serial number found: 19705
Duplicate atom serial number found: 19706
Duplicate atom serial number found: 19707
Duplicate atom serial number found: 19708
1 messages similar to the above omitted
Ignored bad PDB record found on line 104203
ATOM 1970a O T3P X7202 28.096 36.169 -53.231 0.00 0.00 C6 O
Ignored bad PDB record found on line 104204
ATOM 1970b H1 T3P X7202 28.886 36.628 -53.518 0.00 0.00 C6 H
Ignored bad PDB record found on line 104205
ATOM 1970c H2 T3P X7202 28.328 35.803 -52.377 0.00 0.00 C6 H
Ignored bad PDB record found on line 104206
ATOM 1970d O T3P X7203 15.707 -35.426 -29.020 0.00 0.00 C6 O
Ignored bad PDB record found on line 104207
ATOM 1970e H1 T3P X7203 15.647 -34.934 -29.839 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19710
Duplicate atom serial number found: 19711
Duplicate atom serial number found: 19712
Duplicate atom serial number found: 19713
Duplicate atom serial number found: 19714
5 messages similar to the above omitted
Ignored bad PDB record found on line 104219
ATOM 1971a H1 T3P X7207 4.239 43.221 32.745 0.00 0.00 C6 H
Ignored bad PDB record found on line 104220
ATOM 1971b H2 T3P X7207 4.876 43.387 31.382 0.00 0.00 C6 H
Ignored bad PDB record found on line 104221
ATOM 1971c O T3P X7208 9.001 -13.821 41.249 0.00 0.00 C6 O
Ignored bad PDB record found on line 104222
ATOM 1971d H1 T3P X7208 9.010 -13.022 40.723 0.00 0.00 C6 H
Ignored bad PDB record found on line 104223
ATOM 1971e H2 T3P X7208 9.690 -14.367 40.870 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19720
Duplicate atom serial number found: 19721
Ignored bad PDB record found on line 104227
ATOM 19722 O T3P X720a 49.394 31.775 -44.902 0.00 0.00 C6 O
Ignored bad PDB record found on line 104228
ATOM 19723 H1 T3P X720a 48.798 31.760 -44.152 0.00 0.00 C6 H
Ignored bad PDB record found on line 104229
ATOM 19724 H2 T3P X720a 49.921 30.982 -44.804 0.00 0.00 C6 H
Ignored bad PDB record found on line 104230
ATOM 19725 O T3P X720b 14.693 49.641 -15.932 0.00 0.00 C6 O
Ignored bad PDB record found on line 104231
ATOM 19726 H1 T3P X720b 14.447 50.438 -15.461 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19734
Duplicate atom serial number found: 19735
Duplicate atom serial number found: 19736
Duplicate atom serial number found: 19737
Duplicate atom serial number found: 19738
1 messages similar to the above omitted
Ignored bad PDB record found on line 104251
ATOM 1973a O T3P X7212 29.286 2.679 -20.812 0.00 0.00 C6 O
Ignored bad PDB record found on line 104252
ATOM 1973b H1 T3P X7212 29.171 1.785 -20.492 0.00 0.00 C6 H
Ignored bad PDB record found on line 104253
ATOM 1973c H2 T3P X7212 28.593 2.792 -21.463 0.00 0.00 C6 H
Ignored bad PDB record found on line 104254
ATOM 1973d O T3P X7213 -20.482 24.669 -44.222 0.00 0.00 C6 O
Ignored bad PDB record found on line 104255
ATOM 1973e H1 T3P X7213 -21.331 25.110 -44.224 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19740
Duplicate atom serial number found: 19741
Duplicate atom serial number found: 19742
Duplicate atom serial number found: 19743
Duplicate atom serial number found: 19744
5 messages similar to the above omitted
Ignored bad PDB record found on line 104267
ATOM 1974a H1 T3P X7217 6.162 -56.008 48.167 0.00 0.00 C6 H
Ignored bad PDB record found on line 104268
ATOM 1974b H2 T3P X7217 6.937 -57.183 48.724 0.00 0.00 C6 H
Ignored bad PDB record found on line 104269
ATOM 1974c O T3P X7218 -37.462 13.727 49.345 0.00 0.00 C6 O
Ignored bad PDB record found on line 104270
ATOM 1974d H1 T3P X7218 -38.203 14.176 48.939 0.00 0.00 C6 H
Ignored bad PDB record found on line 104271
ATOM 1974e H2 T3P X7218 -36.783 13.724 48.670 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19750
Duplicate atom serial number found: 19751
Ignored bad PDB record found on line 104275
ATOM 19752 O T3P X721a 34.984 19.633 -34.453 0.00 0.00 C6 O
Ignored bad PDB record found on line 104276
ATOM 19753 H1 T3P X721a 35.878 19.296 -34.384 0.00 0.00 C6 H
Ignored bad PDB record found on line 104277
ATOM 19754 H2 T3P X721a 35.046 20.351 -35.083 0.00 0.00 C6 H
Ignored bad PDB record found on line 104278
ATOM 19755 O T3P X721b 37.081 -45.930 12.469 0.00 0.00 C6 O
Ignored bad PDB record found on line 104279
ATOM 19756 H1 T3P X721b 37.631 -45.629 13.192 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19764
Duplicate atom serial number found: 19765
Duplicate atom serial number found: 19766
Duplicate atom serial number found: 19767
Duplicate atom serial number found: 19768
1 messages similar to the above omitted
Ignored bad PDB record found on line 104299
ATOM 1976a O T3P X7222 26.436 -33.856 -50.090 0.00 0.00 C6 O
Ignored bad PDB record found on line 104300
ATOM 1976b H1 T3P X7222 25.992 -34.435 -49.470 0.00 0.00 C6 H
Ignored bad PDB record found on line 104301
ATOM 1976c H2 T3P X7222 27.222 -34.338 -50.348 0.00 0.00 C6 H
Ignored bad PDB record found on line 104302
ATOM 1976d O T3P X7223 41.656 -20.248 -35.954 0.00 0.00 C6 O
Ignored bad PDB record found on line 104303
ATOM 1976e H1 T3P X7223 41.547 -21.185 -36.118 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19770
Duplicate atom serial number found: 19771
Duplicate atom serial number found: 19772
Duplicate atom serial number found: 19773
Duplicate atom serial number found: 19774
5 messages similar to the above omitted
Ignored bad PDB record found on line 104315
ATOM 1977a H1 T3P X7227 -10.004 27.114 6.119 0.00 0.00 C6 H
Ignored bad PDB record found on line 104316
ATOM 1977b H2 T3P X7227 -9.086 28.182 6.676 0.00 0.00 C6 H
Ignored bad PDB record found on line 104317
ATOM 1977c O T3P X7228 36.535 -38.266 -8.134 0.00 0.00 C6 O
Ignored bad PDB record found on line 104318
ATOM 1977d H1 T3P X7228 35.877 -38.198 -7.442 0.00 0.00 C6 H
Ignored bad PDB record found on line 104319
ATOM 1977e H2 T3P X7228 36.242 -37.652 -8.806 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19780
Duplicate atom serial number found: 19781
Ignored bad PDB record found on line 104323
ATOM 19782 O T3P X722a 9.951 -40.196 -16.555 0.00 0.00 C6 O
Ignored bad PDB record found on line 104324
ATOM 19783 H1 T3P X722a 9.006 -40.343 -16.591 0.00 0.00 C6 H
Ignored bad PDB record found on line 104325
ATOM 19784 H2 T3P X722a 10.334 -41.012 -16.877 0.00 0.00 C6 H
Ignored bad PDB record found on line 104326
ATOM 19785 O T3P X722b -37.541 0.010 -46.577 0.00 0.00 C6 O
Ignored bad PDB record found on line 104327
ATOM 19786 H1 T3P X722b -36.923 -0.637 -46.237 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19794
Duplicate atom serial number found: 19795
Duplicate atom serial number found: 19796
Duplicate atom serial number found: 19797
Duplicate atom serial number found: 19798
1 messages similar to the above omitted
Ignored bad PDB record found on line 104347
ATOM 1979a O T3P X7232 -0.663 -27.977 3.383 0.00 0.00 C6 O
Ignored bad PDB record found on line 104348
ATOM 1979b H1 T3P X7232 -0.521 -28.869 3.700 0.00 0.00 C6 H
Ignored bad PDB record found on line 104349
ATOM 1979c H2 T3P X7232 -1.541 -27.994 3.003 0.00 0.00 C6 H
Ignored bad PDB record found on line 104350
ATOM 1979d O T3P X7233 48.879 50.309 -6.705 0.00 0.00 C6 O
Ignored bad PDB record found on line 104351
ATOM 1979e H1 T3P X7233 48.072 50.477 -6.218 0.00 0.00 C6 H
97 messages similar to the above omitted
Duplicate atom serial number found: 19800
Duplicate atom serial number found: 19801
Duplicate atom serial number found: 19802
Duplicate atom serial number found: 19803
Duplicate atom serial number found: 19804
5 messages similar to the above omitted
Ignored bad PDB record found on line 104459
ATOM 1980a H1 T3P X7257 28.268 -32.939 39.799 0.00 0.00 C6 H
Ignored bad PDB record found on line 104460
ATOM 1980b H2 T3P X7257 26.863 -32.416 39.589 0.00 0.00 C6 H
Ignored bad PDB record found on line 104461
ATOM 1980c O T3P X7258 26.151 48.899 48.311 0.00 0.00 C6 O
Ignored bad PDB record found on line 104462
ATOM 1980d H1 T3P X7258 25.461 49.484 47.999 0.00 0.00 C6 H
Ignored bad PDB record found on line 104463
ATOM 1980e H2 T3P X7258 26.693 48.734 47.539 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19810
Duplicate atom serial number found: 19811
Ignored bad PDB record found on line 104467
ATOM 19812 O T3P X725a 26.361 51.003 -17.192 0.00 0.00 C6 O
Ignored bad PDB record found on line 104468
ATOM 19813 H1 T3P X725a 27.055 51.273 -17.793 0.00 0.00 C6 H
Ignored bad PDB record found on line 104469
ATOM 19814 H2 T3P X725a 26.801 50.902 -16.348 0.00 0.00 C6 H
Ignored bad PDB record found on line 104470
ATOM 19815 O T3P X725b 44.463 16.970 0.504 0.00 0.00 C6 O
Ignored bad PDB record found on line 104471
ATOM 19816 H1 T3P X725b 44.214 16.316 -0.150 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19824
Duplicate atom serial number found: 19825
Duplicate atom serial number found: 19826
Duplicate atom serial number found: 19827
Duplicate atom serial number found: 19828
1 messages similar to the above omitted
Ignored bad PDB record found on line 104491
ATOM 1982a O T3P X7262 -35.869 -32.039 33.701 0.00 0.00 C6 O
Ignored bad PDB record found on line 104492
ATOM 1982b H1 T3P X7262 -36.207 -32.052 34.596 0.00 0.00 C6 H
Ignored bad PDB record found on line 104493
ATOM 1982c H2 T3P X7262 -36.275 -31.268 33.303 0.00 0.00 C6 H
Ignored bad PDB record found on line 104494
ATOM 1982d O T3P X7263 17.761 -57.870 51.745 0.00 0.00 C6 O
Ignored bad PDB record found on line 104495
ATOM 1982e H1 T3P X7263 17.656 -58.529 51.058 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19830
Duplicate atom serial number found: 19831
Duplicate atom serial number found: 19832
Duplicate atom serial number found: 19833
Duplicate atom serial number found: 19834
5 messages similar to the above omitted
Ignored bad PDB record found on line 104507
ATOM 1983a H1 T3P X7267 -24.521 -53.844 -10.199 0.00 0.00 C6 H
Ignored bad PDB record found on line 104508
ATOM 1983b H2 T3P X7267 -25.625 -54.857 -9.984 0.00 0.00 C6 H
Ignored bad PDB record found on line 104509
ATOM 1983c O T3P X7268 28.966 -28.798 -28.415 0.00 0.00 C6 O
Ignored bad PDB record found on line 104510
ATOM 1983d H1 T3P X7268 29.109 -27.946 -28.003 0.00 0.00 C6 H
Ignored bad PDB record found on line 104511
ATOM 1983e H2 T3P X7268 29.741 -29.311 -28.182 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19840
Duplicate atom serial number found: 19841
Ignored bad PDB record found on line 104515
ATOM 19842 O T3P X726a 36.569 -35.511 41.015 0.00 0.00 C6 O
Ignored bad PDB record found on line 104516
ATOM 19843 H1 T3P X726a 37.128 -35.586 40.242 0.00 0.00 C6 H
Ignored bad PDB record found on line 104517
ATOM 19844 H2 T3P X726a 37.104 -35.851 41.732 0.00 0.00 C6 H
Ignored bad PDB record found on line 104518
ATOM 19845 O T3P X726b 27.833 -41.044 -48.923 0.00 0.00 C6 O
Ignored bad PDB record found on line 104519
ATOM 19846 H1 T3P X726b 27.203 -40.555 -49.452 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19854
Duplicate atom serial number found: 19855
Duplicate atom serial number found: 19856
Duplicate atom serial number found: 19857
Duplicate atom serial number found: 19858
1 messages similar to the above omitted
Ignored bad PDB record found on line 104539
ATOM 1985a O T3P X7272 14.187 31.354 43.259 0.00 0.00 C6 O
Ignored bad PDB record found on line 104540
ATOM 1985b H1 T3P X7272 14.300 32.201 42.828 0.00 0.00 C6 H
Ignored bad PDB record found on line 104541
ATOM 1985c H2 T3P X7272 13.378 31.445 43.761 0.00 0.00 C6 H
Ignored bad PDB record found on line 104542
ATOM 1985d O T3P X7273 -42.546 -8.137 -36.638 0.00 0.00 C6 O
Ignored bad PDB record found on line 104543
ATOM 1985e H1 T3P X7273 -42.393 -7.912 -37.556 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19860
Duplicate atom serial number found: 19861
Duplicate atom serial number found: 19862
Duplicate atom serial number found: 19863
Duplicate atom serial number found: 19864
5 messages similar to the above omitted
Ignored bad PDB record found on line 104555
ATOM 1986a H1 T3P X7277 16.027 51.708 17.358 0.00 0.00 C6 H
Ignored bad PDB record found on line 104556
ATOM 1986b H2 T3P X7277 15.354 51.031 16.184 0.00 0.00 C6 H
Ignored bad PDB record found on line 104557
ATOM 1986c O T3P X7278 -46.021 46.899 14.455 0.00 0.00 C6 O
Ignored bad PDB record found on line 104558
ATOM 1986d H1 T3P X7278 -45.188 47.142 14.051 0.00 0.00 C6 H
Ignored bad PDB record found on line 104559
ATOM 1986e H2 T3P X7278 -45.777 46.503 15.291 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19870
Duplicate atom serial number found: 19871
Ignored bad PDB record found on line 104563
ATOM 19872 O T3P X727a 26.673 -50.849 -16.847 0.00 0.00 C6 O
Ignored bad PDB record found on line 104564
ATOM 19873 H1 T3P X727a 26.480 -51.382 -16.076 0.00 0.00 C6 H
Ignored bad PDB record found on line 104565
ATOM 19874 H2 T3P X727a 25.924 -50.984 -17.427 0.00 0.00 C6 H
Ignored bad PDB record found on line 104566
ATOM 19875 O T3P X727b 18.274 43.073 -18.308 0.00 0.00 C6 O
Ignored bad PDB record found on line 104567
ATOM 19876 H1 T3P X727b 17.620 43.535 -18.833 0.00 0.00 C6 H
13 messages similar to the above omitted
Duplicate atom serial number found: 19884
Duplicate atom serial number found: 19885
Duplicate atom serial number found: 19886
Duplicate atom serial number found: 19887
Duplicate atom serial number found: 19888
1 messages similar to the above omitted
Ignored bad PDB record found on line 104587
ATOM 1988a O T3P X7282 -36.322 -15.188 -19.842 0.00 0.00 C6 O
Ignored bad PDB record found on line 104588
ATOM 1988b H1 T3P X7282 -36.429 -15.199 -18.891 0.00 0.00 C6 H
Ignored bad PDB record found on line 104589
ATOM 1988c H2 T3P X7282 -35.501 -14.718 -19.986 0.00 0.00 C6 H
Ignored bad PDB record found on line 104590
ATOM 1988d O T3P X7283 35.593 -28.240 -13.172 0.00 0.00 C6 O
Ignored bad PDB record found on line 104591
ATOM 1988e H1 T3P X7283 36.010 -28.392 -14.020 0.00 0.00 C6 H
1 messages similar to the above omitted
Duplicate atom serial number found: 19890
Duplicate atom serial number found: 19891
Duplicate atom serial number found: 19892
Duplicate atom serial number found: 19893
Duplicate atom serial number found: 19894
5 messages similar to the above omitted
Ignored bad PDB record found on line 104603
ATOM 1989a H1 T3P X7287 45.046 39.383 -36.877 0.00 0.00 C6 H
Ignored bad PDB record found on line 104604
ATOM 1989b H2 T3P X7287 44.174 40.172 -37.830 0.00 0.00 C6 H
Ignored bad PDB record found on line 104605
ATOM 1989c O T3P X7288 -31.851 29.311 48.647 0.00 0.00 C6 O
Ignored bad PDB record found on line 104606
ATOM 1989d H1 T3P X7288 -32.714 29.081 48.303 0.00 0.00 C6 H
Ignored bad PDB record found on line 104607
ATOM 1989e H2 T3P X7288 -31.234 28.877 48.059 0.00 0.00 C6 H
16164 messages similar to the above omitted
Chain information for 3MCV_MCV_1d_all.pdb #1
---
Chain | Description
A B C D | No description available
Computing secondary structure
> hide atoms
> color bychain
> set bgColor white
> select /A
4110 atoms, 4146 bonds, 272 residues, 1 model selected
> select ::name="MCV"
167 atoms, 175 bonds, 4 residues, 1 model selected
> show sel atoms
> select ::name="NAP"
292 atoms, 308 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel lime
> style sel sphere
Changed 292 atom styles
> select ::name="MCV"
167 atoms, 175 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 167 atom styles
> color sel magenta
> select /B ::name = "MCV"
41 atoms, 43 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /B ::name = "NAP"
73 atoms, 77 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C ::name = "NAP"
73 atoms, 77 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /C ::name = "MCV"
42 atoms, 44 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D ::name = "MCV"
42 atoms, 44 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D ::name = "NAP"
73 atoms, 77 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /A
4110 atoms, 4146 bonds, 272 residues, 1 model selected
> color sel light gray
> select /B
4113 atoms, 4148 bonds, 273 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ffffffff
> color sel #fffffff9
> color sel #fffffff6
[Repeated 3 time(s)]
> color sel #fffffff4
> color sel #fffffff3
> color sel #fffffff2
> color sel #fffffff0
> color sel #ffffffef
> color sel #ffffffee
> color sel #ffffffed
> color sel #ffffffec
> color sel #ffffffeb
> color sel #ffffffea
[Repeated 3 time(s)]
> color sel #ffffffed
> color sel #fffffff0
> color sel #fffffff5
> color sel #fffffff7
> color sel #fffffff8
> color sel #fffffff9
[Repeated 6 time(s)]
> color sel #fffffffa
> color sel #fffffffb
[Repeated 1 time(s)]
> color sel #fffffffc
> color sel #fffffffd
[Repeated 1 time(s)]
> color sel #fffffffe
> color sel #ffffffff
> color sel #ff2600ff
> color sel #ff9300ff
> color sel #ff7e79ff
[Repeated 1 time(s)]
> color sel #ff7e79f7
> color sel #ff7e79f2
> color sel #ff7e79ee
> color sel #ff7e79eb
> color sel #ff7e79e9
> color sel #ff7e79e8
[Repeated 3 time(s)]
> color sel #ff7e79e7
> color sel #ff7e79e6
> color sel #ff7e79e5
[Repeated 2 time(s)]
> color sel #ff7e79e4
[Repeated 1 time(s)]
> color sel #ff7e79e3
[Repeated 2 time(s)]
> color sel #ff7e79e2
[Repeated 1 time(s)]
> color sel #ff7e79e1
> color sel #ff7e79df
> color sel #ff7e79dd
> color sel #ff7e79da
[Repeated 1 time(s)]
> color sel #ff7e79d9
[Repeated 3 time(s)]
> color sel #ff7e79d8
[Repeated 1 time(s)]
> color sel #ff7e79d7
> color sel #ff7e79d5
> color sel #ff7e79d4
[Repeated 2 time(s)]
> color sel #ff7e79d3
> color sel #ff7e79d2
> color sel #ff7e79c9
> color sel #ff7e79c0
> color sel #ff7e79bb
> color sel #ff7e79b8
> color sel #ff7e79b5
[Repeated 1 time(s)]
> color sel #ff7e79b3
> color sel #ff7e79b1
> color sel #ff7e79af
> color sel #ff7e79ab
> color sel #ff7e79a9
> color sel #ff7e79a6
> color sel #ff7e79a1
> color sel #ff7e79a0
> color sel #ff7e799c
> color sel #ff7e799a
> color sel #ff7e7998
> color sel #ff7e7996
> color sel #ff7e7994
> color sel #ff7e7991
> color sel #ff7e7990
> color sel #ff7e798d
> color sel #ff7e798b
> color sel #ff7e7988
> color sel #ff7e7984
> color sel #ff7e7981
> color sel #ff7e7980
> color sel #ff7e7976
> color sel #ff7e7973
> color sel #ff7e7970
> color sel #ff7e796f
[Repeated 2 time(s)]
> color sel #ff7e796e
> color sel #ff7e796d
> color sel #ff7e796b
> color sel #ff7e796a
> color sel #ff7e7968
> color sel #ff7e7967
> color sel #ff7e7966
[Repeated 4 time(s)]
> color sel #ff7e7965
> color sel #ff7e7964
> color sel #ff7e7963
[Repeated 3 time(s)]
> color sel #ff7e7962
> color sel #ff7e7961
[Repeated 1 time(s)]
> color sel #ff7e795f
> color sel #ff7e795e
> color sel #ff7e795d
> color sel #ff7e795b
[Repeated 2 time(s)]
> color sel #ff7e795c
> color sel #ff7e795d
[Repeated 3 time(s)]
> color sel #ff7e795e
[Repeated 1 time(s)]
> color sel #ff7e7960
> color sel #ff7e7963
> color sel #ff7e7968
> color sel #ff7e796e
> color sel #ff7e7974
> color sel #ff7e7976
> color sel #ff7e7979
> color sel #ff7e797a
[Repeated 2 time(s)]
> color sel #ff7e797b
[Repeated 2 time(s)]
> color sel #ff7e797c
> color sel #ff7e797d
[Repeated 1 time(s)]
> color sel #ff7e797e
[Repeated 1 time(s)]
> color sel #ff7e797f
> color sel #ff7e7980
> color sel #ff7e7975
> color sel #ff7e7971
> color sel #ff7e796e
[Repeated 4 time(s)]
> color sel #ff7e796d
[Repeated 4 time(s)]
> color sel #ff7e796c
[Repeated 3 time(s)]
> color sel #ff7e796b
> color sel #ff7e796a
> color sel #ff7e7969
> color sel #ff7e7968
> color sel #ff7e7967
[Repeated 2 time(s)]
> color sel #ff7e7966
> color sel #ff7e7965
[Repeated 1 time(s)]
> color sel #ff7e7963
[Repeated 7 time(s)]
> color sel #ff7e7962
[Repeated 1 time(s)]
> color sel #ff7e7961
[Repeated 1 time(s)]
> color sel #ff7e7960
[Repeated 1 time(s)]
> color sel #ff7e795f
[Repeated 2 time(s)]
> color sel #ff7e795e
[Repeated 9 time(s)]
> color sel #ff7e795d
[Repeated 1 time(s)]
> color sel #ff7e795c
[Repeated 7 time(s)]
> color sel #ff7e795b
[Repeated 2 time(s)]
> color sel #ff7e795a
[Repeated 2 time(s)]
> color sel #ff7e7959
[Repeated 6 time(s)]
> color sel #ff7e7958
> color sel #ff7e7957
[Repeated 1 time(s)]
> color sel #ff7e7956
[Repeated 1 time(s)]
> color sel #ff7e7955
[Repeated 1 time(s)]
> color sel #ff7e7954
> color sel #ff7e7953
> color sel #ff7e7952
> color sel #ff7e7951
> color sel #ff7e7950
[Repeated 7 time(s)]
> color sel #ff7e794f
[Repeated 2 time(s)]
> color sel #ff7e794e
[Repeated 4 time(s)]
> color sel #ff7e794d
[Repeated 3 time(s)]
> color sel #ff7e794c
[Repeated 5 time(s)]
> color sel #ff7e794b
[Repeated 3 time(s)]
> color sel #ff7e794a
[Repeated 3 time(s)]
> color sel #ff7e7949
> color sel #ff7e7947
[Repeated 2 time(s)]
> color sel #ff7e7949
[Repeated 1 time(s)]
> color sel #ff7e794a
> color sel #ff7e794b
[Repeated 1 time(s)]
> color sel #ff7e794c
[Repeated 1 time(s)]
> color sel #ff7e794d
[Repeated 3 time(s)]
> color sel #ff7e794e
> color sel #ff7e794f
> color sel #ff7e7950
> color sel #ff7e7951
> color sel #ff7e7952
[Repeated 2 time(s)]
> color sel #ff7e7953
[Repeated 1 time(s)]
> color sel #ff7e7954
[Repeated 1 time(s)]
> color sel #ff7e7955
[Repeated 3 time(s)]
> color sel #ff7e7954
[Repeated 1 time(s)]
> color sel #ff7e7953
> color sel #ff7e7951
> color sel #ff7e794e
> color sel #ff7e794c
> color sel #ff7e794a
> color sel #ff7e7948
[Repeated 3 time(s)]
> color sel #ff7e7947
[Repeated 3 time(s)]
> color sel #ff7e7946
> color sel #ff7e7944
> color sel #ff7e7943
[Repeated 5 time(s)]
> color sel #ff7e7942
> color sel #ff7e7941
[Repeated 2 time(s)]
> color sel #ff7e7942
> color sel #ff7e7943
[Repeated 3 time(s)]
> color sel #ff7e7944
> color sel #ff7e7945
> color sel #ff7e7946
> color sel #ff7e7947
> select /C
4101 atoms, 4138 bonds, 271 residues, 1 model selected
> color sel #d4fb79ff
> color sel #73fa79ff
> color sel #00f900ff
> color sel #8efa00ff
> color sel #008f00ff
> color sel #4f8f00ff
> color sel #929000ff
> color sel #009051ff
> color sel #009193ff
[Repeated 1 time(s)]
> color sel #009193f6
> color sel #009193f2
> color sel #009193ee
> color sel #009193ec
> color sel #009193ea
> color sel #009193e9
[Repeated 1 time(s)]
> color sel #009193e8
[Repeated 1 time(s)]
> color sel #009193e7
> color sel #009193e6
> color sel #009193e4
> color sel #009193e0
> color sel #009193de
> color sel #009193da
> color sel #009193d5
> color sel #009193d3
> color sel #009193d1
> color sel #009193cf
[Repeated 1 time(s)]
> color sel #009193ce
[Repeated 3 time(s)]
> color sel #009193cd
> color sel #009193cc
[Repeated 3 time(s)]
> color sel #009193cb
> color sel #009193ca
> color sel #009193c8
> color sel #009193c6
> color sel #009193c1
> color sel #009193be
> color sel #009193bc
> color sel #009193bb
> color sel #009193b9
> color sel #009193b7
> color sel #009193b6
> color sel #009193b4
> color sel #009193b1
> color sel #009193ae
> color sel #009193ac
> color sel #009193aa
> color sel #009193a9
> color sel #009193a7
> color sel #009193a6
> color sel #009193a4
> color sel #009193a2
> color sel #009193a1
> color sel #0091939f
> color sel #0091939e
> color sel #0091939d
> color sel #0091939c
> color sel #0091939b
> color sel #0091939a
> color sel #00919398
> color sel #00919397
> color sel #00919395
> color sel #00919394
> color sel #00919393
> color sel #00919392
> color sel #00919391
> color sel #0091938f
> color sel #0091938d
> color sel #0091938c
> color sel #0091938a
> color sel #00919389
[Repeated 1 time(s)]
> color sel #00919388
> color sel #00919387
> color sel #00919386
> color sel #00919385
> color sel #00919384
> color sel #00919382
> color sel #00919381
> color sel #00919380
> color sel #00919377
> color sel #00919376
> color sel #00919375
> color sel #00919374
> color sel #00919373
> color sel #00919370
[Repeated 1 time(s)]
> color sel #0091936e
> color sel #0091936c
> color sel #0091936b
> color sel #0091936a
[Repeated 1 time(s)]
> color sel #00919369
[Repeated 1 time(s)]
> color sel #00919368
[Repeated 4 time(s)]
> color sel #00919367
[Repeated 3 time(s)]
> color sel #00919366
[Repeated 2 time(s)]
> color sel #00919365
[Repeated 1 time(s)]
> color sel #00919364
[Repeated 5 time(s)]
> color sel #00919363
[Repeated 1 time(s)]
> color sel #00919362
[Repeated 1 time(s)]
> color sel #00919361
[Repeated 5 time(s)]
> color sel #00919360
[Repeated 3 time(s)]
> color sel #0091935f
[Repeated 9 time(s)]
> color sel #0091935e
[Repeated 3 time(s)]
> color sel #0091935d
> color sel #0091935c
> color sel #0091935b
[Repeated 1 time(s)]
> color sel #0091935a
> color sel #00919359
[Repeated 2 time(s)]
> color sel #00919358
[Repeated 1 time(s)]
> color sel #00919357
> color sel #00919356
[Repeated 7 time(s)]
> color sel #00919355
[Repeated 1 time(s)]
> color sel #00919354
[Repeated 1 time(s)]
> color sel #00919353
[Repeated 1 time(s)]
> color sel #00919352
[Repeated 3 time(s)]
> color sel #00919351
[Repeated 4 time(s)]
> color sel #0091934f
> color sel #0091934a
> color sel #00919346
> color sel #00919345
> color sel #00919344
[Repeated 2 time(s)]
> color sel #00919343
> color sel #00919342
[Repeated 3 time(s)]
> color sel #00919343
[Repeated 1 time(s)]
> color sel #00919344
[Repeated 1 time(s)]
> color sel #00919345
[Repeated 8 time(s)]
> color sel #00919346
[Repeated 1 time(s)]
> color sel #00919347
[Repeated 2 time(s)]
> color sel #73fa79ff
[Repeated 1 time(s)]
> color sel #73fa79fc
> color sel #73fa79f6
> color sel #73fa79f1
> color sel #73fa79ea
> color sel #73fa79e4
> color sel #73fa79e3
> color sel #73fa79df
> color sel #73fa79de
[Repeated 3 time(s)]
> color sel #73fa79dd
[Repeated 3 time(s)]
> color sel #73fa79dc
> color sel #73fa79db
> color sel #73fa79da
> color sel #73fa79d9
> color sel #73fa79d7
> color sel #73fa79d4
> color sel #73fa79d2
> color sel #73fa79ce
> color sel #73fa79cc
> color sel #73fa79ca
> color sel #73fa79c8
> color sel #73fa79c5
> color sel #73fa79c3
> color sel #73fa79c1
> color sel #73fa79be
> color sel #73fa79bb
> color sel #73fa79b9
> color sel #73fa79b8
> color sel #73fa79b7
> color sel #73fa79b6
> color sel #73fa79b5
[Repeated 1 time(s)]
> color sel #73fa79b4
> color sel #73fa79b3
> color sel #73fa79b1
> color sel #73fa79b0
> color sel #73fa79ae
> color sel #73fa79ac
> color sel #73fa79aa
> color sel #73fa79a9
> color sel #73fa79a8
[Repeated 1 time(s)]
> color sel #73fa79a7
[Repeated 1 time(s)]
> color sel #73fa79a6
> color sel #73fa79a5
> color sel #73fa79a3
> color sel #73fa79a1
> color sel #73fa799f
> color sel #73fa799e
> color sel #73fa799d
[Repeated 2 time(s)]
> color sel #73fa799c
[Repeated 1 time(s)]
> color sel #73fa799b
> color sel #73fa7999
> color sel #73fa7998
> color sel #73fa7996
> color sel #73fa7995
> color sel #73fa7994
[Repeated 2 time(s)]
> color sel #73fa7993
> color sel #008f00ff
> color sel #009051ff
> color sel #008f00ff
> color sel #929000ff
> color sel #009051ff
[Repeated 1 time(s)]
> color sel #009051fb
> color sel #009051f3
> color sel #009051ee
> color sel #009051eb
> color sel #009051e7
> color sel #009051e6
[Repeated 1 time(s)]
> color sel #009051e5
[Repeated 1 time(s)]
> color sel #009051e4
> color sel #009051e3
> color sel #009051e2
> color sel #009051de
> color sel #009051dc
> color sel #009051d9
> color sel #009051d5
> color sel #009051d2
> color sel #009051d0
> color sel #009051cd
> color sel #009051cc
> color sel #009051ca
> color sel #009051c4
> color sel #009051c1
> color sel #009051bc
> color sel #009051ba
> color sel #009051b6
> color sel #009051b4
> color sel #009051b3
[Repeated 2 time(s)]
> color sel #009051b2
> color sel #009051b1
> color sel #009051af
> color sel #009051ad
> color sel #009051ac
> color sel #009051aa
> color sel #009051a9
> color sel #009051a8
> color sel #009051a6
> color sel #009051a5
[Repeated 1 time(s)]
> color sel #009051a4
[Repeated 1 time(s)]
> color sel #009051a3
[Repeated 2 time(s)]
> color sel #009051a2
> color sel #009051a1
> color sel #009051a0
> color sel #0090519e
> color sel #0090519d
> color sel #0090519c
> color sel #0090519b
> color sel #00905199
> color sel #00905196
> color sel #00905194
> color sel #00905192
> color sel #0090518f
> color sel #0090518d
> color sel #0090518b
> color sel #00905189
[Repeated 1 time(s)]
> color sel #00905188
[Repeated 5 time(s)]
> color sel #00905187
> color sel #00905186
[Repeated 1 time(s)]
> color sel #00905184
> color sel #00905183
> color sel #00905181
> color sel #00905180
> color sel #00905177
> color sel #00905176
> color sel #00905174
> color sel #00905173
> color sel #00905172
> color sel #00905171
> color sel #00905170
> color sel #0090516f
> color sel #0090516e
> color sel #0090516c
[Repeated 3 time(s)]
> color sel #0090516b
[Repeated 4 time(s)]
> color sel #0090516a
> color sel #00905169
> color sel #00905167
> color sel #00905166
[Repeated 6 time(s)]
> color sel #00905165
[Repeated 1 time(s)]
> color sel #00905164
[Repeated 1 time(s)]
> color sel #00905163
[Repeated 1 time(s)]
> color sel #00905162
> color sel #00905161
[Repeated 2 time(s)]
> color sel #00905160
[Repeated 2 time(s)]
> color sel #0090515f
[Repeated 1 time(s)]
> color sel #0090515e
[Repeated 2 time(s)]
> color sel #0090515d
[Repeated 1 time(s)]
> color sel #0090515c
[Repeated 4 time(s)]
> color sel #0090515b
[Repeated 6 time(s)]
> color sel #0090515a
[Repeated 2 time(s)]
> color sel #00905159
[Repeated 6 time(s)]
> color sel #00905158
> color sel #00905157
> color sel #00905156
> color sel #00905155
> color sel #00905154
> color sel #00905153
[Repeated 5 time(s)]
> color sel #00905152
[Repeated 1 time(s)]
> color sel #00905151
[Repeated 2 time(s)]
> color sel #00905150
[Repeated 5 time(s)]
> color sel #0090514f
[Repeated 8 time(s)]
> color sel #0090514e
[Repeated 4 time(s)]
> color sel #0090514d
> color sel #0090514c
[Repeated 2 time(s)]
> color sel #0090514b
[Repeated 3 time(s)]
> color sel #0090514a
> color sel #00905149
> color sel #00905148
> color sel #00905147
> color sel #00905146
[Repeated 3 time(s)]
> color sel #00905148
> color sel #0090514a
> color sel #0090514d
> color sel #0090514e
> color sel #0090514f
> color sel #00905150
[Repeated 1 time(s)]
> color sel #0090514f
> color sel #0090514e
[Repeated 1 time(s)]
> color sel #0090514d
> color sel #0090514c
[Repeated 4 time(s)]
> color sel #0090514b
[Repeated 3 time(s)]
> color sel #0090514a
[Repeated 2 time(s)]
> color sel #00905149
[Repeated 6 time(s)]
> color sel #00905148
[Repeated 2 time(s)]
> color sel #00905147
> select /D
4108 atoms, 4144 bonds, 272 residues, 1 model selected
> color sel orange
> color sel #ff9300ff
[Repeated 1 time(s)]
> color sel #ff9300f6
> color sel #ff9300ee
> color sel #ff9300e5
> color sel #ff9300d9
> color sel #ff9300d4
> color sel #ff9300cf
> color sel #ff9300cb
> color sel #ff9300ca
[Repeated 2 time(s)]
> color sel #ff9300c8
> color sel #ff9300c5
> color sel #ff9300c1
> color sel #ff9300bb
> color sel #ff9300b5
> color sel #ff9300ab
> color sel #ff9300a7
> color sel #ff9300a1
> color sel #ff9300a0
> color sel #ff93009c
> color sel #ff93009a
> color sel #ff930099
> color sel #ff930096
> color sel #ff930093
> color sel #ff930091
> color sel #ff93008e
> color sel #ff93008b
> color sel #ff930088
> color sel #ff930087
> color sel #ff930085
> color sel #ff930084
> color sel #ff930083
> color sel #ff930082
> color sel #ff930081
> color sel #ff930080
> color sel #ff930077
[Repeated 1 time(s)]
> color sel #ff930076
[Repeated 1 time(s)]
> color sel #ff930075
> color sel #ff930073
> color sel #ff930072
> color sel #ff93006f
> color sel #ff93006d
> color sel #ff93006a
> color sel #ff930068
> color sel #ff930067
> color sel #ff930065
> color sel #ff930063
> color sel #ff930062
> color sel #ff930061
[Repeated 3 time(s)]
> color sel #ff930060
> color sel #ff93005f
> color sel #ff93005d
> color sel #ff93005b
> color sel #ff93005a
> color sel #ff930059
> color sel #ff930057
> color sel #ff930056
[Repeated 4 time(s)]
> color sel #ff930055
> color sel #ff930054
> color sel #ff930053
[Repeated 1 time(s)]
> color sel #ff930052
> color sel #ff930051
> color sel #ff93004f
> color sel #ff93004e
> color sel #ff93004d
[Repeated 1 time(s)]
> color sel #ff93004c
> color sel #ff93004b
[Repeated 1 time(s)]
> color sel #ff93004a
[Repeated 5 time(s)]
> color sel #ff930049
[Repeated 2 time(s)]
> color sel #ff930048
[Repeated 3 time(s)]
> color sel #ff930047
[Repeated 2 time(s)]
> color sel #ff930046
[Repeated 5 time(s)]
> color sel #ff930045
[Repeated 2 time(s)]
> color sel #ff930044
[Repeated 1 time(s)]
> color sel #ff930043
> color sel #ff930042
> color sel #ff930041
> color sel #ff930040
> color sel #ff93003f
[Repeated 2 time(s)]
> color sel #ff93003e
[Repeated 3 time(s)]
> color sel #ff93003d
> color sel #ff93003c
> color sel #ff93003a
> color sel #ff930039
> color sel #ff930038
[Repeated 2 time(s)]
> color sel #ff930037
[Repeated 1 time(s)]
> color sel #ff930036
> color sel #ff930034
> color sel #ff930032
> color sel #ff930031
[Repeated 1 time(s)]
> color sel #ff93002f
> color sel #ff93002e
> color sel #ff93002d
> color sel #ff93002c
[Repeated 2 time(s)]
> color sel #ff93002e
[Repeated 1 time(s)]
> color sel #ff93002f
[Repeated 1 time(s)]
> color sel #ff930030
> color sel #ff930031
[Repeated 1 time(s)]
> color sel #ff930032
> color sel #ff930033
> color sel #ff930035
> color sel #ff930036
> color sel #ff930037
> color sel #ff930038
[Repeated 5 time(s)]
> color sel #ff930039
[Repeated 1 time(s)]
> color sel #ff93003a
> color sel #ff93003b
[Repeated 3 time(s)]
> color sel #ff93003c
[Repeated 2 time(s)]
> color sel #ff93003d
[Repeated 4 time(s)]
> color sel #ff93003e
[Repeated 1 time(s)]
> color sel #ff93003f
> color sel #ff930040
[Repeated 6 time(s)]
> color sel #ff930041
[Repeated 5 time(s)]
> color sel #ff930042
[Repeated 6 time(s)]
> color sel #ff930043
[Repeated 9 time(s)]
> color sel #ff930044
[Repeated 9 time(s)]
> color sel #ff930045
[Repeated 5 time(s)]
> color sel #ff930046
> color sel #ff930047
> color sel #ff930048
[Repeated 1 time(s)]
> color sel #ff930047
> select /A ::name="MCV"
42 atoms, 44 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel magenta
> select /A ::name="NAP"
73 atoms, 77 bonds, 1 residue, 1 model selected
> color sel lime
> select /C
4101 atoms, 4138 bonds, 271 residues, 1 model selected
> color sel blue
> color sel #76d6ffff
> color sel #0096ffff
> color sel #0433ffff
[Repeated 1 time(s)]
> color sel #0433fff1
> color sel #0433ffe7
> color sel #0433ffdd
> color sel #0433ffd2
> color sel #0433ffce
> color sel #0433ffcd
> color sel #0433ffca
> color sel #0433ffc9
> color sel #0433ffc8
> color sel #0433ffc7
> color sel #0433ffc6
> color sel #0433ffc5
> color sel #0433ffc4
> color sel #0433ffc2
> color sel #0433ffc0
> color sel #0433ffbd
> color sel #0433ffbc
> color sel #0433ffb9
> color sel #0433ffb7
> color sel #0433ffb4
> color sel #0433ffb2
> color sel #0433ffb0
> color sel #0433ffae
> color sel #0433ffab
> color sel #0433ffa7
> color sel #0433ffa3
> color sel #0433ffa1
> color sel #0433ff9f
> color sel #0433ff9e
> color sel #0433ff9c
> color sel #0433ff9b
> color sel #0433ff9a
[Repeated 1 time(s)]
> color sel #0433ff99
[Repeated 1 time(s)]
> color sel #0433ff98
> color sel #0433ff97
> color sel #0433ff95
> color sel #0433ff94
> color sel #0433ff92
> color sel #0433ff90
> color sel #0433ff8f
> color sel #0433ff8d
> color sel #0433ff8c
> color sel #0433ff8b
[Repeated 1 time(s)]
> color sel #0433ff89
> color sel #0433ff88
[Repeated 1 time(s)]
> color sel #0433ff87
> color sel #0433ff86
> color sel #0433ff85
[Repeated 2 time(s)]
> color sel #0433ff84
[Repeated 3 time(s)]
> color sel #0433ff83
> color sel #0433ff82
[Repeated 1 time(s)]
> color sel #0433ff81
> color sel #0433ff80
> color sel #0433ff76
> color sel #0433ff75
> color sel #0433ff74
> color sel #0433ff73
> color sel #0433ff72
[Repeated 2 time(s)]
> color sel #0433ff71
[Repeated 4 time(s)]
> color sel #0433ff70
[Repeated 1 time(s)]
> color sel #0433ff6f
[Repeated 3 time(s)]
> color sel #0433ff6e
[Repeated 1 time(s)]
> color sel #0433ff6d
> color sel #0433ff6c
[Repeated 2 time(s)]
> color sel #0433ff6b
[Repeated 1 time(s)]
> color sel #0433ff6a
[Repeated 2 time(s)]
> color sel #0433ff69
[Repeated 2 time(s)]
> color sel #0433ff68
[Repeated 3 time(s)]
> color sel #0433ff67
[Repeated 2 time(s)]
> color sel #0433ff66
[Repeated 2 time(s)]
> color sel #0433ff65
[Repeated 1 time(s)]
> color sel #0433ff64
> color sel #0433ff63
[Repeated 5 time(s)]
> color sel #0433ff62
[Repeated 6 time(s)]
> color sel #0433ff61
> color sel #0433ff60
[Repeated 2 time(s)]
> color sel #0433ff5f
[Repeated 3 time(s)]
> color sel #0433ff5e
[Repeated 4 time(s)]
> color sel #0433ff5d
[Repeated 3 time(s)]
> color sel #0433ff5c
[Repeated 1 time(s)]
> color sel #0433ff5b
[Repeated 3 time(s)]
> color sel #0433ff5a
[Repeated 3 time(s)]
> color sel #0433ff59
[Repeated 1 time(s)]
> color sel #0433ff58
[Repeated 1 time(s)]
> color sel #0433ff57
[Repeated 3 time(s)]
> color sel #0433ff56
[Repeated 3 time(s)]
> color sel #0433ff55
[Repeated 2 time(s)]
> color sel #0433ff54
[Repeated 4 time(s)]
> color sel #0433ff53
[Repeated 4 time(s)]
> color sel #0433ff52
[Repeated 1 time(s)]
> color sel #0433ff51
[Repeated 1 time(s)]
> color sel #0433ff50
[Repeated 5 time(s)]
> color sel #0433ff4f
[Repeated 1 time(s)]
> color sel #0433ff4e
> color sel #0433ff4c
[Repeated 2 time(s)]
> color sel #0433ff4b
[Repeated 3 time(s)]
> color sel #0433ff4a
> color sel #0433ff49
[Repeated 2 time(s)]
> color sel #0433ff47
> select /C
4101 atoms, 4138 bonds, 271 residues, 1 model selected
> select /C:249
10 atoms, 9 bonds, 1 residue, 1 model selected
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV_GIF.obj"
> select /C
4101 atoms, 4138 bonds, 271 residues, 1 model selected
> color sel forest green
> select /C:156
19 atoms, 18 bonds, 1 residue, 1 model selected
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV_GIF.obj"
> select main
15945 atoms, 16069 bonds, 1076 residues, 1 model selected
> lighting shadows true
> lighting full
> lighting shadows false
> lighting full
> select /C:132
20 atoms, 20 bonds, 1 residue, 1 model selected
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV_GIF.obj"
> select /A
4110 atoms, 4146 bonds, 272 residues, 1 model selected
> select /B
4113 atoms, 4148 bonds, 273 residues, 1 model selected
> hide sel cartoons
> select /C
4101 atoms, 4138 bonds, 271 residues, 1 model selected
> hide sel cartoons
> select /D
4108 atoms, 4144 bonds, 272 residues, 1 model selected
> hide sel cartoons
> view
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV.A_GIF.obj"
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV.A_GIF.jpg" width 936 height 739 supersample
> 3
> select helix
6793 atoms, 6804 bonds, 443 residues, 1 model selected
> color sel cyan
> color sel cornflower blue
> color sel purple
> color sel dark gray
> color sel dim gray
> select clear
> select strand
2290 atoms, 2274 bonds, 144 residues, 1 model selected
> color sel yellow
> select /A:202
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:202
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:159
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV.A_ligs_sec_struct.obj"
> select /A :NAP :MCV
115 atoms, 121 bonds, 2 residues, 1 model selected
> hide sel atoms
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV.A_sec_struct.obj"
> view sel
No displayed objects specified.
> select /A :NAP :MCV
115 atoms, 121 bonds, 2 residues, 1 model selected
> show sel atoms
> select /A:269@C6A
1 atom, 1 residue, 1 model selected
> select strand
2290 atoms, 2274 bonds, 144 residues, 1 model selected
> color sel light gray
> select strand
2290 atoms, 2274 bonds, 144 residues, 1 model selected
> select strand
2290 atoms, 2274 bonds, 144 residues, 1 model selected
> select helix
6793 atoms, 6804 bonds, 443 residues, 1 model selected
> color sel light gray
> select /A:236
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:269@N6A
1 atom, 1 residue, 1 model selected
> select clear
> save "/Users/fionaoyatsi/OneDrive - Universität Münster/University of
> Munster/Mitarbaiter Seminar/3MCV.A_ligs.gif" width 936 height 739
> supersample 3
> open "/Users/fionaoyatsi/Library/CloudStorage/OneDrive-
> UniversitätMünster/Alignment/Rationalization/Journals/Dynophore
> Interpretation/dynophore/Crystal
> Structures/PYR/4CMJ.A_UIH_a/Dynophore/2012/Ligand-
> chainA-4CMJ.A-2012_dynophore.json"
Failed opening file /Users/fionaoyatsi/Library/CloudStorage/OneDrive-
UniversitätMünster/Alignment/Rationalization/Journals/Dynophore
Interpretation/dynophore/Crystal
Structures/PYR/4CMJ.A_UIH_a/Dynophore/2012/Ligand-
chainA-4CMJ.A-2012_dynophore.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/fionaoyatsi/Library/CloudStorage/OneDrive-
UniversitätMünster/Alignment/Rationalization/Journals/Dynophore
Interpretation/dynophore/Crystal
Structures/PYR/4CMJ.A_UIH_a/Dynophore/2012/Ligand-
chainA-4CMJ.A-2012_dynophore.json structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open "/Users/fionaoyatsi/Library/CloudStorage/OneDrive-
> UniversitätMünster/Alignment/Rationalization/Journals/Dynophore
> Interpretation/dynophore/Crystal
> Structures/PYR/4CMJ.A_UIH_a/Dynophore/2012/Ligand-
> chainA-4CMJ.A-2012_dynophore.json"
Failed opening file /Users/fionaoyatsi/Library/CloudStorage/OneDrive-
UniversitätMünster/Alignment/Rationalization/Journals/Dynophore
Interpretation/dynophore/Crystal
Structures/PYR/4CMJ.A_UIH_a/Dynophore/2012/Ligand-
chainA-4CMJ.A-2012_dynophore.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/fionaoyatsi/Library/CloudStorage/OneDrive-
UniversitätMünster/Alignment/Rationalization/Journals/Dynophore
Interpretation/dynophore/Crystal
Structures/PYR/4CMJ.A_UIH_a/Dynophore/2012/Ligand-
chainA-4CMJ.A-2012_dynophore.json structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/fionaoyatsi/Desktop/movie1.mp4
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1394, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1312, in save_spin_movie
run(session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,6
Model Number: MX2K3D/A
Chip: Apple M4 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 26 days, 4 hours, 15 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 23 hours ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission Denied |
comment:2 by , 23 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Fiona,
--Eric