Opened 5 years ago

Closed 5 years ago

#3225 closed defect (fixed)

Failure reading DCD: unexpected end of data

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: MD/Ensemble Analysis Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0 (2020-05-09)
Description
Trying to read the trajectory of a SARS-CoV-2 spike protein simulation from https://www.deshawresearch.com/downloads/download_trajectory_sarscov2.cgi/. Note that for each trajectory the coordinate PDB file is messed up, with a TER after each and every atom beyond chain A (but remove those lines and the coordinates open fine). Attempting to load one of the DCDs fails (this trajectory is split into 9x733MB DCD files, in case it's relevant).

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 1.0rc202005090702 (2020-05-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> open /run/media/tic20/storage/structure_dump/covid-19/de_shaw/DESRES-
> Trajectory_sarscov2-11021566-no-water-zinc-glueCA/system_stripped.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/covid-19/de_shaw/DESRES-
Trajectory_sarscov2-11021566-no-water-zinc-glueCA/system_stripped.pdb  
---  
warnings | Ignored bad PDB record found on line 60190  
ATOM 186a0 O4_6 NM5 C1171 42.722 -12.917 -65.328 1.00 0.00 O  
  
Ignored bad PDB record found on line 60191  
ATOM 186a2 C5 NM5 C1171 28.542 -1.043 -57.066 1.00 0.00 C  
  
Ignored bad PDB record found on line 60192  
ATOM 186a4 C5_1 NM5 C1171 30.583 -6.545 -56.390 1.00 0.00 C  
  
Ignored bad PDB record found on line 60193  
ATOM 186a6 C5_2 NM5 C1171 36.214 -8.281 -57.188 1.00 0.00 C  
  
Ignored bad PDB record found on line 60194  
ATOM 186a8 C5_3 NM5 C1171 32.859 -12.246 -54.295 1.00 0.00 C  
  
43 messages similar to the above omitted  
Duplicate atom serial number found: 18700  
Duplicate atom serial number found: 18702  
Duplicate atom serial number found: 18704  
Duplicate atom serial number found: 18706  
Duplicate atom serial number found: 18708  
Ignored bad PDB record found on line 60243  
ATOM 1870a H61 NM5 C1171 30.544 -8.527 -55.702 1.00 0.00 H  
  
Ignored bad PDB record found on line 60244  
ATOM 1870c H61 NM5 C1171 37.048 -6.773 -58.506 1.00 0.00 H  
  
Ignored bad PDB record found on line 60245  
ATOM 1870e H61 NM5 C1171 41.239 -10.476 -59.729 1.00 0.00 H  
  
Duplicate atom serial number found: 18710  
Duplicate atom serial number found: 18712  
Duplicate atom serial number found: 18714  
Duplicate atom serial number found: 18716  
Duplicate atom serial number found: 18718  
Ignored bad PDB record found on line 60251  
ATOM 1871a H62 NM5 C1171 38.170 -7.921 -57.746 1.00 0.00 H  
  
Ignored bad PDB record found on line 60252  
ATOM 1871c H62 NM5 C1171 40.707 -11.916 -60.480 1.00 0.00 H  
  
Ignored bad PDB record found on line 60253  
ATOM 1871e H62 NM5 C1171 44.431 -14.299 -62.932 1.00 0.00 H  
  
Duplicate atom serial number found: 18720  
Duplicate atom serial number found: 18722  
Duplicate atom serial number found: 18724  
Duplicate atom serial number found: 18726  
Duplicate atom serial number found: 18728  
Ignored bad PDB record found on line 60259  
ATOM 1872a H4O NM5 C1171 32.297 -9.951 -65.815 1.00 0.00 H  
  
Ignored bad PDB record found on line 60260  
ATOM 1872c H4O NM5 C1171 31.988 -15.244 -55.074 1.00 0.00 H  
  
Ignored bad PDB record found on line 60261  
ATOM 1872e H6O NM5 C1171 28.683 1.436 -57.334 1.00 0.00 H  
  
Duplicate atom serial number found: 18730  
Duplicate atom serial number found: 18732  
Duplicate atom serial number found: 18734  
Duplicate atom serial number found: 18736  
Duplicate atom serial number found: 18738  
Ignored bad PDB record found on line 60267  
ATOM 1873a H1_2 NM5 C1171 34.296 -7.622 -55.563 1.00 0.00 H  
  
Ignored bad PDB record found on line 60268  
ATOM 1873c H1_3 NM5 C1171 36.052 -11.300 -53.844 1.00 0.00 H  
  
Ignored bad PDB record found on line 60269  
ATOM 1873e H1_4 NM5 C1171 37.657 -7.281 -60.589 1.00 0.00 H  
  
Duplicate atom serial number found: 18740  
Duplicate atom serial number found: 18742  
Duplicate atom serial number found: 18744  
Duplicate atom serial number found: 18746  
Duplicate atom serial number found: 18748  
Ignored bad PDB record found on line 60275  
ATOM 1874a H2_4 NM5 C1171 36.043 -8.680 -61.767 1.00 0.00 H  
  
Ignored bad PDB record found on line 60276  
ATOM 1874c H2_5 NM5 C1171 36.137 -12.357 -65.099 1.00 0.00 H  
  
Ignored bad PDB record found on line 60277  
ATOM 1874e H2_6 NM5 C1171 42.756 -8.905 -62.852 1.00 0.00 H  
  
Duplicate atom serial number found: 18750  
Duplicate atom serial number found: 18752  
Duplicate atom serial number found: 18754  
Duplicate atom serial number found: 18756  
Duplicate atom serial number found: 18758  
Ignored bad PDB record found on line 60283  
ATOM 1875a H3_6 NM5 C1171 41.766 -10.648 -64.392 1.00 0.00 H  
  
Ignored bad PDB record found on line 60284  
ATOM 1875c H4_1 NM5 C1171 32.530 -6.129 -55.518 1.00 0.00 H  
  
Ignored bad PDB record found on line 60285  
ATOM 1875e H4_2 NM5 C1171 36.097 -10.443 -57.825 1.00 0.00 H  
  
Duplicate atom serial number found: 18760  
Duplicate atom serial number found: 18762  
Duplicate atom serial number found: 18764  
Duplicate atom serial number found: 18766  
Duplicate atom serial number found: 18768  
Ignored bad PDB record found on line 60291  
ATOM 1876a H5_2 NM5 C1171 36.591 -7.756 -56.311 1.00 0.00 H  
  
Ignored bad PDB record found on line 60292  
ATOM 1876c H5_3 NM5 C1171 32.767 -12.036 -55.360 1.00 0.00 H  
  
Ignored bad PDB record found on line 60293  
ATOM 1876e H5_4 NM5 C1171 38.692 -10.782 -59.472 1.00 0.00 H  
  
Duplicate atom serial number found: 18770  
Duplicate atom serial number found: 18772  
Duplicate atom serial number found: 18774  
Duplicate atom serial number found: 18776  
Duplicate atom serial number found: 18778  
Ignored bad PDB record found on line 60299  
ATOM 1877a O NLM C1172 22.594 -15.820 -45.332 1.00 0.00 O  
  
Ignored bad PDB record found on line 60300  
ATOM 1877c CB NLM C1172 24.411 -17.029 -47.275 1.00 0.00 C  
  
Ignored bad PDB record found on line 60301  
ATOM 1877e CG NLM C1172 25.028 -18.301 -46.604 1.00 0.00 C  
  
Duplicate atom serial number found: 18780  
Duplicate atom serial number found: 18782  
Duplicate atom serial number found: 18784  
Duplicate atom serial number found: 18786  
Duplicate atom serial number found: 18788  
Ignored bad PDB record found on line 60307  
ATOM 1878a HB3 NLM C1172 24.861 -16.797 -48.240 1.00 0.00 H  
  
Ignored bad PDB record found on line 60308  
ATOM 1878c HD21 NLM C1172 26.589 -18.066 -47.825 1.00 0.00 H  
  
Ignored bad PDB record found on line 60309  
ATOM 1878e CME NM5 C1173 25.056 -21.256 -49.304 1.00 0.00 C  
  
Duplicate atom serial number found: 18790  
Duplicate atom serial number found: 18792  
Duplicate atom serial number found: 18794  
Duplicate atom serial number found: 18796  
Duplicate atom serial number found: 18798  
Ignored bad PDB record found on line 60315  
ATOM 1879a C1_4 NM5 C1173 40.324 -26.119 -45.537 1.00 0.00 C  
  
Ignored bad PDB record found on line 60316  
ATOM 1879c C1_5 NM5 C1173 40.697 -29.263 -49.026 1.00 0.00 C  
  
Ignored bad PDB record found on line 60317  
ATOM 1879e C1_6 NM5 C1173 45.411 -27.445 -43.076 1.00 0.00 C  
  
Ignored bad PDB record found on line 60318  
ATOM 187a0 C2 NM5 C1173 27.161 -20.865 -46.976 1.00 0.00 C  
  
Ignored bad PDB record found on line 60319  
ATOM 187a2 C2_1 NM5 C1173 32.939 -22.478 -45.379 1.00 0.00 C  
  
46 messages similar to the above omitted  
Duplicate atom serial number found: 18800  
Duplicate atom serial number found: 18802  
Duplicate atom serial number found: 18804  
Duplicate atom serial number found: 18806  
Duplicate atom serial number found: 18808  
Ignored bad PDB record found on line 60371  
ATOM 1880a O5 NM5 C1173 28.398 -18.823 -46.511 1.00 0.00 O  
  
Ignored bad PDB record found on line 60372  
ATOM 1880c O5_1 NM5 C1173 31.093 -23.893 -45.964 1.00 0.00 O  
  
Ignored bad PDB record found on line 60373  
ATOM 1880e O5_2 NM5 C1173 36.322 -26.075 -44.925 1.00 0.00 O  
  
Duplicate atom serial number found: 18810  
Duplicate atom serial number found: 18812  
Duplicate atom serial number found: 18814  
Duplicate atom serial number found: 18816  
Duplicate atom serial number found: 18818  
Ignored bad PDB record found on line 60379  
ATOM 1881a C6_1 NM5 C1173 31.098 -26.273 -46.258 1.00 0.00 C  
  
Ignored bad PDB record found on line 60380  
ATOM 1881c C6_2 NM5 C1173 38.462 -26.140 -43.941 1.00 0.00 C  
  
Ignored bad PDB record found on line 60381  
ATOM 1881e C6_3 NM5 C1173 31.618 -30.355 -41.631 1.00 0.00 C  
  
Duplicate atom serial number found: 18820  
Duplicate atom serial number found: 18822  
Duplicate atom serial number found: 18824  
Duplicate atom serial number found: 18826  
Duplicate atom serial number found: 18828  
Ignored bad PDB record found on line 60387  
ATOM 1882a O6_2 NM5 C1173 39.071 -26.791 -45.156 1.00 0.00 O  
  
Ignored bad PDB record found on line 60388  
ATOM 1882c O6_3 NM5 C1173 31.795 -30.883 -40.280 1.00 0.00 O  
  
Ignored bad PDB record found on line 60389  
ATOM 1882e O6_4 NM5 C1173 44.288 -27.356 -43.962 1.00 0.00 O  
  
Duplicate atom serial number found: 18830  
Duplicate atom serial number found: 18832  
Duplicate atom serial number found: 18834  
Duplicate atom serial number found: 18836  
Duplicate atom serial number found: 18838  
Ignored bad PDB record found on line 60395  
ATOM 1883a H4 NM5 C1173 30.065 -20.970 -47.481 1.00 0.00 H  
  
Ignored bad PDB record found on line 60396  
ATOM 1883c H5 NM5 C1173 29.689 -19.396 -44.907 1.00 0.00 H  
  
Ignored bad PDB record found on line 60397  
ATOM 1883e H1M NM5 C1173 25.841 -21.697 -49.917 1.00 0.00 H  
  
Duplicate atom serial number found: 18840  
Duplicate atom serial number found: 18842  
Duplicate atom serial number found: 18844  
Duplicate atom serial number found: 18846  
Duplicate atom serial number found: 18848  
Ignored bad PDB record found on line 60403  
ATOM 1884a H2O NM5 C1173 34.490 -29.334 -46.108 1.00 0.00 H  
  
Ignored bad PDB record found on line 60404  
ATOM 1884c H2O NM5 C1173 41.245 -25.105 -48.050 1.00 0.00 H  
  
Ignored bad PDB record found on line 60405  
ATOM 1884e H2O NM5 C1173 48.587 -26.366 -43.327 1.00 0.00 H  
  
Duplicate atom serial number found: 18850  
Duplicate atom serial number found: 18852  
Duplicate atom serial number found: 18854  
Duplicate atom serial number found: 18856  
Duplicate atom serial number found: 18858  
Ignored bad PDB record found on line 60411  
ATOM 1885a H3O NM5 C1173 35.439 -24.470 -45.068 1.00 0.00 H  
  
Ignored bad PDB record found on line 60412  
ATOM 1885c H3O NM5 C1173 47.554 -26.367 -46.407 1.00 0.00 H  
  
Ignored bad PDB record found on line 60413  
ATOM 1885e H3O NM5 C1173 42.673 -28.732 -53.144 1.00 0.00 H  
  
Duplicate atom serial number found: 18860  
Duplicate atom serial number found: 18862  
Duplicate atom serial number found: 18864  
Duplicate atom serial number found: 18866  
Duplicate atom serial number found: 18868  
Ignored bad PDB record found on line 60419  
ATOM 1886a H61 NM5 C1173 47.128 -31.638 -44.269 1.00 0.00 H  
  
Ignored bad PDB record found on line 60420  
ATOM 1886c H61 NM5 C1173 38.736 -25.772 -51.239 1.00 0.00 H  
  
Ignored bad PDB record found on line 60421  
ATOM 1886e H61 NM5 C1173 31.641 -29.268 -41.697 1.00 0.00 H  
  
Duplicate atom serial number found: 18870  
Duplicate atom serial number found: 18872  
Duplicate atom serial number found: 18874  
Duplicate atom serial number found: 18876  
Duplicate atom serial number found: 18878  
Ignored bad PDB record found on line 60427  
ATOM 1887a H62 NM5 C1173 37.831 -27.252 -51.403 1.00 0.00 H  
  
Ignored bad PDB record found on line 60428  
ATOM 1887c H62 NM5 C1173 30.647 -30.638 -42.037 1.00 0.00 H  
  
Ignored bad PDB record found on line 60429  
ATOM 1887e H4O NM5 C1173 37.618 -29.396 -42.298 1.00 0.00 H  
  
Duplicate atom serial number found: 18880  
Duplicate atom serial number found: 18882  
Duplicate atom serial number found: 18884  
Duplicate atom serial number found: 18886  
Duplicate atom serial number found: 18888  
Ignored bad PDB record found on line 60435  
ATOM 1888a H6O NM5 C1173 29.575 -25.475 -47.094 1.00 0.00 H  
  
Ignored bad PDB record found on line 60436  
ATOM 1888c H6O NM5 C1173 45.915 -32.540 -42.307 1.00 0.00 H  
  
Ignored bad PDB record found on line 60437  
ATOM 1888e H6O NM5 C1173 37.818 -27.056 -48.838 1.00 0.00 H  
  
Duplicate atom serial number found: 18890  
Duplicate atom serial number found: 18892  
Duplicate atom serial number found: 18894  
Duplicate atom serial number found: 18896  
Duplicate atom serial number found: 18898  
Ignored bad PDB record found on line 60443  
ATOM 1889a H1_5 NM5 C1173 40.452 -30.078 -48.344 1.00 0.00 H  
  
Ignored bad PDB record found on line 60444  
ATOM 1889c H1_6 NM5 C1173 45.269 -26.954 -42.113 1.00 0.00 H  
  
Ignored bad PDB record found on line 60445  
ATOM 1889e H2_1 NM5 C1173 32.776 -22.479 -44.301 1.00 0.00 H  
  
Ignored bad PDB record found on line 60446  
ATOM 188a0 H2_2 NM5 C1173 33.628 -28.184 -44.796 1.00 0.00 H  
  
Ignored bad PDB record found on line 60447  
ATOM 188a2 H2_3 NM5 C1173 36.274 -32.577 -43.289 1.00 0.00 H  
  
46 messages similar to the above omitted  
Duplicate atom serial number found: 18900  
Duplicate atom serial number found: 18902  
Duplicate atom serial number found: 18904  
Duplicate atom serial number found: 18906  
Duplicate atom serial number found: 18908  
Ignored bad PDB record found on line 60499  
ATOM 1890a C2N NM5 C1175 25.953 22.394 -53.297 1.00 0.00 C  
  
Ignored bad PDB record found on line 60500  
ATOM 1890c N2 NM5 C1175 22.299 15.171 -53.989 1.00 0.00 N  
  
Ignored bad PDB record found on line 60501  
ATOM 1890e N2_1 NM5 C1175 26.894 21.481 -53.086 1.00 0.00 N  
  
Duplicate atom serial number found: 18910  
Duplicate atom serial number found: 18912  
Duplicate atom serial number found: 18914  
Duplicate atom serial number found: 18916  
Duplicate atom serial number found: 18918  
Ignored bad PDB record found on line 60507  
ATOM 1891a O2N NM5 C1175 21.582 13.281 -53.579 1.00 0.00 O  
  
Ignored bad PDB record found on line 60508  
ATOM 1891c O2N NM5 C1175 24.918 22.501 -52.583 1.00 0.00 O  
  
Ignored bad PDB record found on line 60509  
ATOM 1891e C3 NM5 C1175 23.806 17.142 -53.609 1.00 0.00 C  
  
Duplicate atom serial number found: 18920  
Duplicate atom serial number found: 18922  
Duplicate atom serial number found: 18924  
Duplicate atom serial number found: 18926  
Duplicate atom serial number found: 18928  
Ignored bad PDB record found on line 60515  
ATOM 1892a C3_6 NM5 C1175 34.725 28.877 -42.322 1.00 0.00 C  
  
Ignored bad PDB record found on line 60516  
ATOM 1892c O3 NM5 C1175 24.806 16.292 -52.986 1.00 0.00 O  
  
Ignored bad PDB record found on line 60517  
ATOM 1892e O3_1 NM5 C1175 28.491 21.654 -50.632 1.00 0.00 O  
  
Duplicate atom serial number found: 18930  
Duplicate atom serial number found: 18932  
Duplicate atom serial number found: 18934  
Duplicate atom serial number found: 18936  
Duplicate atom serial number found: 18938  
Ignored bad PDB record found on line 60523  
ATOM 1893a C4 NM5 C1175 24.535 18.412 -54.134 1.00 0.00 C  
  
Ignored bad PDB record found on line 60524  
ATOM 1893c C4_1 NM5 C1175 28.047 19.276 -50.137 1.00 0.00 C  
  
Ignored bad PDB record found on line 60525  
ATOM 1893e C4_2 NM5 C1175 30.952 21.018 -45.992 1.00 0.00 C  
  
Duplicate atom serial number found: 18940  
Duplicate atom serial number found: 18942  
Duplicate atom serial number found: 18944  
Duplicate atom serial number found: 18946  
Duplicate atom serial number found: 18948  
Ignored bad PDB record found on line 60531  
ATOM 1894a O4_1 NM5 C1175 29.426 19.166 -49.460 1.00 0.00 O  
  
Ignored bad PDB record found on line 60532  
ATOM 1894c O4_2 NM5 C1175 30.983 21.369 -44.544 1.00 0.00 O  
  
Ignored bad PDB record found on line 60533  
ATOM 1894e O4_3 NM5 C1175 35.439 15.454 -45.171 1.00 0.00 O  
  
Duplicate atom serial number found: 18950  
Duplicate atom serial number found: 18952  
Duplicate atom serial number found: 18954  
Duplicate atom serial number found: 18956  
Duplicate atom serial number found: 18958  
Ignored bad PDB record found on line 60539  
ATOM 1895a C5_2 NM5 C1175 29.730 21.536 -46.738 1.00 0.00 C  
  
Ignored bad PDB record found on line 60540  
ATOM 1895c C5_3 NM5 C1175 33.209 16.094 -45.724 1.00 0.00 C  
  
Ignored bad PDB record found on line 60541  
ATOM 1895e C5_4 NM5 C1175 32.341 24.711 -44.727 1.00 0.00 C  
  
Duplicate atom serial number found: 18960  
Duplicate atom serial number found: 18962  
Duplicate atom serial number found: 18964  
Duplicate atom serial number found: 18966  
Duplicate atom serial number found: 18968  
Ignored bad PDB record found on line 60547  
ATOM 1896a O5_3 NM5 C1175 31.884 16.583 -45.213 1.00 0.00 O  
  
Ignored bad PDB record found on line 60548  
ATOM 1896c O5_4 NM5 C1175 31.104 25.157 -45.441 1.00 0.00 O  
  
Ignored bad PDB record found on line 60549  
ATOM 1896e O5_5 NM5 C1175 34.401 23.860 -49.596 1.00 0.00 O  
  
Duplicate atom serial number found: 18970  
Duplicate atom serial number found: 18972  
Duplicate atom serial number found: 18974  
Duplicate atom serial number found: 18976  
Duplicate atom serial number found: 18978  
Ignored bad PDB record found on line 60555  
ATOM 1897a C6_4 NM5 C1175 32.278 25.149 -43.251 1.00 0.00 C  
  
Ignored bad PDB record found on line 60556  
ATOM 1897c C6_5 NM5 C1175 33.043 23.661 -51.657 1.00 0.00 C  
  
Ignored bad PDB record found on line 60557  
ATOM 1897e C6_6 NM5 C1175 37.073 25.892 -41.930 1.00 0.00 C  
  
Duplicate atom serial number found: 18980  
Duplicate atom serial number found: 18982  
Duplicate atom serial number found: 18984  
Duplicate atom serial number found: 18986  
Duplicate atom serial number found: 18988  
Ignored bad PDB record found on line 60563  
ATOM 1898a O6_5 NM5 C1175 33.773 22.559 -52.123 1.00 0.00 O  
  
Ignored bad PDB record found on line 60564  
ATOM 1898c O6_6 NM5 C1175 36.762 24.524 -41.980 1.00 0.00 O  
  
Ignored bad PDB record found on line 60565  
ATOM 1898e H1 NM5 C1175 21.253 17.254 -55.331 1.00 0.00 H  
  
Duplicate atom serial number found: 18990  
Duplicate atom serial number found: 18992  
Duplicate atom serial number found: 18994  
Duplicate atom serial number found: 18996  
Duplicate atom serial number found: 18998  
Ignored bad PDB record found on line 60571  
ATOM 1899a H1M NM5 C1175 27.151 23.764 -54.433 1.00 0.00 H  
  
Ignored bad PDB record found on line 60572  
ATOM 1899c H2M NM5 C1175 23.757 12.634 -55.179 1.00 0.00 H  
  
Ignored bad PDB record found on line 60573  
ATOM 1899e H2M NM5 C1175 25.454 24.226 -54.248 1.00 0.00 H  
  
Ignored bad PDB record found on line 60574  
ATOM 189a0 H2N NM5 C1175 21.789 15.463 -53.167 1.00 0.00 H  
  
Ignored bad PDB record found on line 60575  
ATOM 189a2 H2N NM5 C1175 27.605 21.243 -53.762 1.00 0.00 H  
  
814 messages similar to the above omitted  
Duplicate atom serial number found: 19000  
Duplicate atom serial number found: 19002  
Duplicate atom serial number found: 19004  
Duplicate atom serial number found: 19006  
Duplicate atom serial number found: 19008  
Ignored bad PDB record found on line 61395  
ATOM 1900a HWS SOL W 88 -62.393 -80.186 87.033 1.00 0.00 H  
  
Ignored bad PDB record found on line 61396  
ATOM 1900c HWS SOL W 88 -62.420 -79.201 88.183 1.00 0.00 H  
  
Ignored bad PDB record found on line 61397  
ATOM 1900e OWS SOL W 89 -83.155 87.937 80.274 1.00 0.00 O  
  
Duplicate atom serial number found: 19010  
Duplicate atom serial number found: 19012  
Duplicate atom serial number found: 19014  
Duplicate atom serial number found: 19016  
Duplicate atom serial number found: 19018  
Ignored bad PDB record found on line 61403  
ATOM 1901a OWS SOL W 91 -73.186 -70.076 -88.768 1.00 0.00 O  
  
Ignored bad PDB record found on line 61404  
ATOM 1901c HWS SOL W 91 -73.664 -70.900 -88.864 1.00 0.00 H  
  
Ignored bad PDB record found on line 61405  
ATOM 1901e HWS SOL W 91 -72.741 -69.958 -89.607 1.00 0.00 H  
  
Duplicate atom serial number found: 19020  
Duplicate atom serial number found: 19022  
Duplicate atom serial number found: 19024  
Duplicate atom serial number found: 19026  
Duplicate atom serial number found: 19028  
Ignored bad PDB record found on line 61411  
ATOM 1902a HWS SOL W 93 -84.443 84.640 87.120 1.00 0.00 H  
  
Ignored bad PDB record found on line 61412  
ATOM 1902c OWS SOL W 94 68.082 89.727 -88.747 1.00 0.00 O  
  
Ignored bad PDB record found on line 61413  
ATOM 1902e HWS SOL W 94 68.395 88.842 -88.561 1.00 0.00 H  
  
Duplicate atom serial number found: 19030  
Duplicate atom serial number found: 19032  
Duplicate atom serial number found: 19034  
Duplicate atom serial number found: 19036  
Duplicate atom serial number found: 19038  
Ignored bad PDB record found on line 61419  
ATOM 1903a HWS SOL W 96 -79.686 -80.867 -87.012 1.00 0.00 H  
  
Ignored bad PDB record found on line 61420  
ATOM 1903c HWS SOL W 96 -79.101 -80.216 -85.777 1.00 0.00 H  
  
Ignored bad PDB record found on line 61421  
ATOM 1903e OWS SOL W 97 -60.491 -46.091 -72.612 1.00 0.00 O  
  
Duplicate atom serial number found: 19040  
Duplicate atom serial number found: 19042  
Duplicate atom serial number found: 19044  
Duplicate atom serial number found: 19046  
Duplicate atom serial number found: 19048  
Ignored bad PDB record found on line 61427  
ATOM 1904a OWS SOL W 99 -80.187 71.187 87.826 1.00 0.00 O  
  
Ignored bad PDB record found on line 61428  
ATOM 1904c HWS SOL W 99 -79.278 71.147 88.123 1.00 0.00 H  
  
Ignored bad PDB record found on line 61429  
ATOM 1904e HWS SOL W 99 -80.288 72.074 87.480 1.00 0.00 H  
  
Duplicate atom serial number found: 19050  
Duplicate atom serial number found: 19052  
Duplicate atom serial number found: 19054  
Duplicate atom serial number found: 19056  
Duplicate atom serial number found: 19058  
Ignored bad PDB record found on line 61435  
ATOM 1905a HWS SOL W 101 -77.843 84.597 -83.912 1.00 0.00 H  
  
Ignored bad PDB record found on line 61436  
ATOM 1905c OWS SOL W 102 -86.259 -71.511 86.955 1.00 0.00 O  
  
Ignored bad PDB record found on line 61437  
ATOM 1905e HWS SOL W 102 -86.821 -71.851 86.259 1.00 0.00 H  
  
Duplicate atom serial number found: 19060  
Duplicate atom serial number found: 19062  
Duplicate atom serial number found: 19064  
Duplicate atom serial number found: 19066  
Duplicate atom serial number found: 19068  
Ignored bad PDB record found on line 61443  
ATOM 1906a HWS SOL W 104 -62.275 -76.841 -86.385 1.00 0.00 H  
  
Ignored bad PDB record found on line 61444  
ATOM 1906c HWS SOL W 104 -61.159 -77.828 -86.653 1.00 0.00 H  
  
Ignored bad PDB record found on line 61445  
ATOM 1906e OWS SOL W 105 -76.763 -69.484 81.164 1.00 0.00 O  
  
Duplicate atom serial number found: 19070  
Duplicate atom serial number found: 19072  
Duplicate atom serial number found: 19074  
Duplicate atom serial number found: 19076  
Duplicate atom serial number found: 19078  
Ignored bad PDB record found on line 61451  
ATOM 1907a OWS SOL W 107 90.217 -87.205 -90.120 1.00 0.00 O  
  
Ignored bad PDB record found on line 61452  
ATOM 1907c HWS SOL W 107 89.752 -86.721 -89.438 1.00 0.00 H  
  
Ignored bad PDB record found on line 61453  
ATOM 1907e HWS SOL W 107 89.526 -87.645 -90.615 1.00 0.00 H  
  

[cut out a _bunch_ of stuff in the middle to get it to fit in the ticket-description length limit]

Duplicate atom serial number found: 18742  
Duplicate atom serial number found: 18744  
Duplicate atom serial number found: 18746  
Duplicate atom serial number found: 18748  
Ignored bad PDB record found on line 60275  
ATOM 1874a H2_4 NM5 C1171 36.043 -8.680 -61.767 1.00 0.00 H  
  
Ignored bad PDB record found on line 60276  
ATOM 1874c H2_5 NM5 C1171 36.137 -12.357 -65.099 1.00 0.00 H  
  
Ignored bad PDB record found on line 60277  
ATOM 1874e H2_6 NM5 C1171 42.756 -8.905 -62.852 1.00 0.00 H  
  
Duplicate atom serial number found: 18750  
Duplicate atom serial number found: 18752  
Duplicate atom serial number found: 18754  
Duplicate atom serial number found: 18756  
Duplicate atom serial number found: 18758  
Ignored bad PDB record found on line 60283  
ATOM 1875a H3_6 NM5 C1171 41.766 -10.648 -64.392 1.00 0.00 H  
  
Ignored bad PDB record found on line 60284  
ATOM 1875c H4_1 NM5 C1171 32.530 -6.129 -55.518 1.00 0.00 H  
  
Ignored bad PDB record found on line 60285  
ATOM 1875e H4_2 NM5 C1171 36.097 -10.443 -57.825 1.00 0.00 H  
  
Duplicate atom serial number found: 18760  
Duplicate atom serial number found: 18762  
Duplicate atom serial number found: 18764  
Duplicate atom serial number found: 18766  
Duplicate atom serial number found: 18768  
Ignored bad PDB record found on line 60291  
ATOM 1876a H5_2 NM5 C1171 36.591 -7.756 -56.311 1.00 0.00 H  
  
Ignored bad PDB record found on line 60292  
ATOM 1876c H5_3 NM5 C1171 32.767 -12.036 -55.360 1.00 0.00 H  
  
Ignored bad PDB record found on line 60293  
ATOM 1876e H5_4 NM5 C1171 38.692 -10.782 -59.472 1.00 0.00 H  
  
Duplicate atom serial number found: 18770  
Duplicate atom serial number found: 18772  
Duplicate atom serial number found: 18774  
Duplicate atom serial number found: 18776  
Duplicate atom serial number found: 18778  
Ignored bad PDB record found on line 60299  
ATOM 1877a O NLM C1172 22.594 -15.820 -45.332 1.00 0.00 O  
  
Ignored bad PDB record found on line 60300  
ATOM 1877c CB NLM C1172 24.411 -17.029 -47.275 1.00 0.00 C  
  
Ignored bad PDB record found on line 60301  
ATOM 1877e CG NLM C1172 25.028 -18.301 -46.604 1.00 0.00 C  
  
Duplicate atom serial number found: 18780  
Duplicate atom serial number found: 18782  
Duplicate atom serial number found: 18784  
Duplicate atom serial number found: 18786  
Duplicate atom serial number found: 18788  
Ignored bad PDB record found on line 60307  
ATOM 1878a HB3 NLM C1172 24.861 -16.797 -48.240 1.00 0.00 H  
  
Ignored bad PDB record found on line 60308  
ATOM 1878c HD21 NLM C1172 26.589 -18.066 -47.825 1.00 0.00 H  
  
Ignored bad PDB record found on line 60309  
ATOM 1878e CME NM5 C1173 25.056 -21.256 -49.304 1.00 0.00 C  
  
Duplicate atom serial number found: 18790  
Duplicate atom serial number found: 18792  
Duplicate atom serial number found: 18794  
Duplicate atom serial number found: 18796  
Duplicate atom serial number found: 18798  
Ignored bad PDB record found on line 60315  
ATOM 1879a C1_4 NM5 C1173 40.324 -26.119 -45.537 1.00 0.00 C  
  
Ignored bad PDB record found on line 60316  
ATOM 1879c C1_5 NM5 C1173 40.697 -29.263 -49.026 1.00 0.00 C  
  
Ignored bad PDB record found on line 60317  
ATOM 1879e C1_6 NM5 C1173 45.411 -27.445 -43.076 1.00 0.00 C  
  
Ignored bad PDB record found on line 60318  
ATOM 187a0 C2 NM5 C1173 27.161 -20.865 -46.976 1.00 0.00 C  
  
Ignored bad PDB record found on line 60319  
ATOM 187a2 C2_1 NM5 C1173 32.939 -22.478 -45.379 1.00 0.00 C  
  
46 messages similar to the above omitted  
Duplicate atom serial number found: 18800  
Duplicate atom serial number found: 18802  
Duplicate atom serial number found: 18804  
Duplicate atom serial number found: 18806  
Duplicate atom serial number found: 18808  
Ignored bad PDB record found on line 60371  
ATOM 1880a O5 NM5 C1173 28.398 -18.823 -46.511 1.00 0.00 O  
  
Ignored bad PDB record found on line 60372  
ATOM 1880c O5_1 NM5 C1173 31.093 -23.893 -45.964 1.00 0.00 O  
  
Ignored bad PDB record found on line 60373  
ATOM 1880e O5_2 NM5 C1173 36.322 -26.075 -44.925 1.00 0.00 O  
  
Duplicate atom serial number found: 18810  
Duplicate atom serial number found: 18812  
Duplicate atom serial number found: 18814  
Duplicate atom serial number found: 18816  
Duplicate atom serial number found: 18818  
Ignored bad PDB record found on line 60379  
ATOM 1881a C6_1 NM5 C1173 31.098 -26.273 -46.258 1.00 0.00 C  
  
Ignored bad PDB record found on line 60380  
ATOM 1881c C6_2 NM5 C1173 38.462 -26.140 -43.941 1.00 0.00 C  
  
Ignored bad PDB record found on line 60381  
ATOM 1881e C6_3 NM5 C1173 31.618 -30.355 -41.631 1.00 0.00 C  
  
Duplicate atom serial number found: 18820  
Duplicate atom serial number found: 18822  
Duplicate atom serial number found: 18824  
Duplicate atom serial number found: 18826  
Duplicate atom serial number found: 18828  
Ignored bad PDB record found on line 60387  
ATOM 1882a O6_2 NM5 C1173 39.071 -26.791 -45.156 1.00 0.00 O  
  
Ignored bad PDB record found on line 60388  
ATOM 1882c O6_3 NM5 C1173 31.795 -30.883 -40.280 1.00 0.00 O  
  
Ignored bad PDB record found on line 60389  
ATOM 1882e O6_4 NM5 C1173 44.288 -27.356 -43.962 1.00 0.00 O  
  
Duplicate atom serial number found: 18830  
Duplicate atom serial number found: 18832  
Duplicate atom serial number found: 18834  
Duplicate atom serial number found: 18836  
Duplicate atom serial number found: 18838  
Ignored bad PDB record found on line 60395  
ATOM 1883a H4 NM5 C1173 30.065 -20.970 -47.481 1.00 0.00 H  
  
Ignored bad PDB record found on line 60396  
ATOM 1883c H5 NM5 C1173 29.689 -19.396 -44.907 1.00 0.00 H  
  
Ignored bad PDB record found on line 60397  
ATOM 1883e H1M NM5 C1173 25.841 -21.697 -49.917 1.00 0.00 H  
  
Duplicate atom serial number found: 18840  
Duplicate atom serial number found: 18842  
Duplicate atom serial number found: 18844  
Duplicate atom serial number found: 18846  
Duplicate atom serial number found: 18848  
Ignored bad PDB record found on line 60403  
ATOM 1884a H2O NM5 C1173 34.490 -29.334 -46.108 1.00 0.00 H  
  
Ignored bad PDB record found on line 60404  
ATOM 1884c H2O NM5 C1173 41.245 -25.105 -48.050 1.00 0.00 H  
  
Ignored bad PDB record found on line 60405  
ATOM 1884e H2O NM5 C1173 48.587 -26.366 -43.327 1.00 0.00 H  
  
Duplicate atom serial number found: 18850  
Duplicate atom serial number found: 18852  
Duplicate atom serial number found: 18854  
Duplicate atom serial number found: 18856  
Duplicate atom serial number found: 18858  
Ignored bad PDB record found on line 60411  
ATOM 1885a H3O NM5 C1173 35.439 -24.470 -45.068 1.00 0.00 H  
  
Ignored bad PDB record found on line 60412  
ATOM 1885c H3O NM5 C1173 47.554 -26.367 -46.407 1.00 0.00 H  
  
Ignored bad PDB record found on line 60413  
ATOM 1885e H3O NM5 C1173 42.673 -28.732 -53.144 1.00 0.00 H  
  
Duplicate atom serial number found: 18860  
Duplicate atom serial number found: 18862  
Duplicate atom serial number found: 18864  
Duplicate atom serial number found: 18866  
Duplicate atom serial number found: 18868  
Ignored bad PDB record found on line 60419  
ATOM 1886a H61 NM5 C1173 47.128 -31.638 -44.269 1.00 0.00 H  
  
Ignored bad PDB record found on line 60420  
ATOM 1886c H61 NM5 C1173 38.736 -25.772 -51.239 1.00 0.00 H  
  
Ignored bad PDB record found on line 60421  
ATOM 1886e H61 NM5 C1173 31.641 -29.268 -41.697 1.00 0.00 H  
  
Duplicate atom serial number found: 18870  
Duplicate atom serial number found: 18872  
Duplicate atom serial number found: 18874  
Duplicate atom serial number found: 18876  
Duplicate atom serial number found: 18878  
Ignored bad PDB record found on line 60427  
ATOM 1887a H62 NM5 C1173 37.831 -27.252 -51.403 1.00 0.00 H  
  
Ignored bad PDB record found on line 60428  
ATOM 1887c H62 NM5 C1173 30.647 -30.638 -42.037 1.00 0.00 H  
  
Ignored bad PDB record found on line 60429  
ATOM 1887e H4O NM5 C1173 37.618 -29.396 -42.298 1.00 0.00 H  
  
Duplicate atom serial number found: 18880  
Duplicate atom serial number found: 18882  
Duplicate atom serial number found: 18884  
Duplicate atom serial number found: 18886  
Duplicate atom serial number found: 18888  
Ignored bad PDB record found on line 60435  
ATOM 1888a H6O NM5 C1173 29.575 -25.475 -47.094 1.00 0.00 H  
  
Ignored bad PDB record found on line 60436  
ATOM 1888c H6O NM5 C1173 45.915 -32.540 -42.307 1.00 0.00 H  
  
Ignored bad PDB record found on line 60437  
ATOM 1888e H6O NM5 C1173 37.818 -27.056 -48.838 1.00 0.00 H  
  
Duplicate atom serial number found: 18890  
Duplicate atom serial number found: 18892  
Duplicate atom serial number found: 18894  
Duplicate atom serial number found: 18896  
Duplicate atom serial number found: 18898  
Ignored bad PDB record found on line 60443  
ATOM 1889a H1_5 NM5 C1173 40.452 -30.078 -48.344 1.00 0.00 H  
  
Ignored bad PDB record found on line 60444  
ATOM 1889c H1_6 NM5 C1173 45.269 -26.954 -42.113 1.00 0.00 H  
  
Ignored bad PDB record found on line 60445  
ATOM 1889e H2_1 NM5 C1173 32.776 -22.479 -44.301 1.00 0.00 H  
  
Ignored bad PDB record found on line 60446  
ATOM 188a0 H2_2 NM5 C1173 33.628 -28.184 -44.796 1.00 0.00 H  
  
Ignored bad PDB record found on line 60447  
ATOM 188a2 H2_3 NM5 C1173 36.274 -32.577 -43.289 1.00 0.00 H  
  
46 messages similar to the above omitted  
Duplicate atom serial number found: 18900  
Duplicate atom serial number found: 18902  
Duplicate atom serial number found: 18904  
Duplicate atom serial number found: 18906  
Duplicate atom serial number found: 18908  
Ignored bad PDB record found on line 60499  
ATOM 1890a C2N NM5 C1175 25.953 22.394 -53.297 1.00 0.00 C  
  
Ignored bad PDB record found on line 60500  
ATOM 1890c N2 NM5 C1175 22.299 15.171 -53.989 1.00 0.00 N  
  
Ignored bad PDB record found on line 60501  
ATOM 1890e N2_1 NM5 C1175 26.894 21.481 -53.086 1.00 0.00 N  
  
Duplicate atom serial number found: 18910  
Duplicate atom serial number found: 18912  
Duplicate atom serial number found: 18914  
Duplicate atom serial number found: 18916  
Duplicate atom serial number found: 18918  
Ignored bad PDB record found on line 60507  
ATOM 1891a O2N NM5 C1175 21.582 13.281 -53.579 1.00 0.00 O  
  
Ignored bad PDB record found on line 60508  
ATOM 1891c O2N NM5 C1175 24.918 22.501 -52.583 1.00 0.00 O  
  
Ignored bad PDB record found on line 60509  
ATOM 1891e C3 NM5 C1175 23.806 17.142 -53.609 1.00 0.00 C  
  
Duplicate atom serial number found: 18920  
Duplicate atom serial number found: 18922  
Duplicate atom serial number found: 18924  
Duplicate atom serial number found: 18926  
Duplicate atom serial number found: 18928  
Ignored bad PDB record found on line 60515  
ATOM 1892a C3_6 NM5 C1175 34.725 28.877 -42.322 1.00 0.00 C  
  
Ignored bad PDB record found on line 60516  
ATOM 1892c O3 NM5 C1175 24.806 16.292 -52.986 1.00 0.00 O  
  
Ignored bad PDB record found on line 60517  
ATOM 1892e O3_1 NM5 C1175 28.491 21.654 -50.632 1.00 0.00 O  
  
Duplicate atom serial number found: 18930  
Duplicate atom serial number found: 18932  
Duplicate atom serial number found: 18934  
Duplicate atom serial number found: 18936  
Duplicate atom serial number found: 18938  
Ignored bad PDB record found on line 60523  
ATOM 1893a C4 NM5 C1175 24.535 18.412 -54.134 1.00 0.00 C  
  
Ignored bad PDB record found on line 60524  
ATOM 1893c C4_1 NM5 C1175 28.047 19.276 -50.137 1.00 0.00 C  
  
Ignored bad PDB record found on line 60525  
ATOM 1893e C4_2 NM5 C1175 30.952 21.018 -45.992 1.00 0.00 C  
  
Duplicate atom serial number found: 18940  
Duplicate atom serial number found: 18942  
Duplicate atom serial number found: 18944  
Duplicate atom serial number found: 18946  
Duplicate atom serial number found: 18948  
Ignored bad PDB record found on line 60531  
ATOM 1894a O4_1 NM5 C1175 29.426 19.166 -49.460 1.00 0.00 O  
  
Ignored bad PDB record found on line 60532  
ATOM 1894c O4_2 NM5 C1175 30.983 21.369 -44.544 1.00 0.00 O  
  
Ignored bad PDB record found on line 60533  
ATOM 1894e O4_3 NM5 C1175 35.439 15.454 -45.171 1.00 0.00 O  
  
Duplicate atom serial number found: 18950  
Duplicate atom serial number found: 18952  
Duplicate atom serial number found: 18954  
Duplicate atom serial number found: 18956  
Duplicate atom serial number found: 18958  
Ignored bad PDB record found on line 60539  
ATOM 1895a C5_2 NM5 C1175 29.730 21.536 -46.738 1.00 0.00 C  
  
Ignored bad PDB record found on line 60540  
ATOM 1895c C5_3 NM5 C1175 33.209 16.094 -45.724 1.00 0.00 C  
  
Ignored bad PDB record found on line 60541  
ATOM 1895e C5_4 NM5 C1175 32.341 24.711 -44.727 1.00 0.00 C  
  
Duplicate atom serial number found: 18960  
Duplicate atom serial number found: 18962  
Duplicate atom serial number found: 18964  
Duplicate atom serial number found: 18966  
Duplicate atom serial number found: 18968  
Ignored bad PDB record found on line 60547  
ATOM 1896a O5_3 NM5 C1175 31.884 16.583 -45.213 1.00 0.00 O  
  
Ignored bad PDB record found on line 60548  
ATOM 1896c O5_4 NM5 C1175 31.104 25.157 -45.441 1.00 0.00 O  
  
Ignored bad PDB record found on line 60549  
ATOM 1896e O5_5 NM5 C1175 34.401 23.860 -49.596 1.00 0.00 O  
  
Duplicate atom serial number found: 18970  
Duplicate atom serial number found: 18972  
Duplicate atom serial number found: 18974  
Duplicate atom serial number found: 18976  
Duplicate atom serial number found: 18978  
Ignored bad PDB record found on line 60555  
ATOM 1897a C6_4 NM5 C1175 32.278 25.149 -43.251 1.00 0.00 C  
  
Ignored bad PDB record found on line 60556  
ATOM 1897c C6_5 NM5 C1175 33.043 23.661 -51.657 1.00 0.00 C  
  
Ignored bad PDB record found on line 60557  
ATOM 1897e C6_6 NM5 C1175 37.073 25.892 -41.930 1.00 0.00 C  
  
Duplicate atom serial number found: 18980  
Duplicate atom serial number found: 18982  
Duplicate atom serial number found: 18984  
Duplicate atom serial number found: 18986  
Duplicate atom serial number found: 18988  
Ignored bad PDB record found on line 60563  
ATOM 1898a O6_5 NM5 C1175 33.773 22.559 -52.123 1.00 0.00 O  
  
Ignored bad PDB record found on line 60564  
ATOM 1898c O6_6 NM5 C1175 36.762 24.524 -41.980 1.00 0.00 O  
  
Ignored bad PDB record found on line 60565  
ATOM 1898e H1 NM5 C1175 21.253 17.254 -55.331 1.00 0.00 H  
  
Duplicate atom serial number found: 18990  
Duplicate atom serial number found: 18992  
Duplicate atom serial number found: 18994  
Duplicate atom serial number found: 18996  
Duplicate atom serial number found: 18998  
Ignored bad PDB record found on line 60571  
ATOM 1899a H1M NM5 C1175 27.151 23.764 -54.433 1.00 0.00 H  
  
Ignored bad PDB record found on line 60572  
ATOM 1899c H2M NM5 C1175 23.757 12.634 -55.179 1.00 0.00 H  
  
Ignored bad PDB record found on line 60573  
ATOM 1899e H2M NM5 C1175 25.454 24.226 -54.248 1.00 0.00 H  
  
Ignored bad PDB record found on line 60574  
ATOM 189a0 H2N NM5 C1175 21.789 15.463 -53.167 1.00 0.00 H  
  
Ignored bad PDB record found on line 60575  
ATOM 189a2 H2N NM5 C1175 27.605 21.243 -53.762 1.00 0.00 H  
  
560 messages similar to the above omitted  
  
Chain information for system_stripped.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> isolde start

> set selectionWidth 4

Chain information for system_stripped.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | No description available  
  
Done loading forcefield  

> open /run/media/tic20/storage/structure_dump/covid-19/de_shaw/DESRES-
> Trajectory_sarscov2-11021566-no-water-zinc-glueCA/sarscov2-11021566-no-
> water-zinc-glueCA/sarscov2-11021566-no-water-zinc-glueCA-0000.dcd

Must specify a structure model to read the coordinates into  

> open /run/media/tic20/storage/structure_dump/covid-19/de_shaw/DESRES-
> Trajectory_sarscov2-11021566-no-water-zinc-glueCA/sarscov2-11021566-no-
> water-zinc-glueCA/sarscov2-11021566-no-water-zinc-glueCA-0000.dcd format dcd

Must specify a structure model to read the coordinates into  

> open sarscov2-11021566-no-water-zinc-glueCA-0000.dcd structureModel #1

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 380, in collated_open  
return func(*func_args, **func_kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/md_crds/__init__.py", line 45, in open  
replace=replace)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/md_crds/read_coords.py", line 34, in read_coords  
dcd = DCD(file_name)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/md_crds/dcd/MDToolsMarch97/md_DCD.py", line 175, in
__init__  
dat = [c.decode('utf-8') for c in up('80c',f.read(cs('80c')))]  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/md_crds/dcd/MDToolsMarch97/md_DCD.py", line 175, in
<listcomp>  
dat = [c.decode('utf-8') for c in up('80c',f.read(cs('80c')))]  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 0:
unexpected end of data  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 0:
unexpected end of data  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/md_crds/dcd/MDToolsMarch97/md_DCD.py", line 175, in  
dat = [c.decode('utf-8') for c in up('80c',f.read(cs('80c')))]  
  
See log for complete Python traceback.  
  

> usage open

open fileNames restOfLine  
— Open/fetch data files  
fileNames: file names to open  
restOfLine: the rest of line

open formats  
— report formats that can be opened  

> open formats

File format| Short name(s)| Suffixes  
---|---|---  
Amira mesh| amira| .am  
APBS potential| apbs| .dx  
AutoDock PDBQT| pdbqt| .pdbqt  
BRIX density map| brix| .brix  
CCP4 density map| ccp4| .ccp4, .map  
Chimera map| cmap| .cmap, .cmp  
ChimeraX commands| cmd| .cxc  
ChimeraX session| session| .cxs  
Clustal ALN sequence| aln or clustal| .aln, .clustal, .clustalw, .clustalx  
CNS or XPLOR density map| xplor| .cns, .xplor  
COLLADA| collada| .dae  
Compiled Python code| compiled python| .pyc, .pyo  
DCD trajectory format| dcd| .dcd  
DelPhi or GRASP potential| delphi| .phi  
DeltaVision map| dv| .dv  
DICOM medical imaging| dicom| .dcm  
Direction dependent resolution values| fsc| .dres  
DOCK scoring grid| dock| .bmp, .cnt, .nrg  
DSN6 density map| dsn6| .omap  
EMAN HDF map| emanhdf| .hdf, .hdf5, .h5  
FASTA sequence| fasta| .fa, .fasta, .afasta, .afa  
Gaussian cube grid| cube| .cube, .cub  
MSF sequence| msf| .msf  
RSF sequence| rsf| .rsf  
glTF| gltf| .glb  
gOpenMol grid| gopenmol| .plt  
Gromacs xtc format| xtc| .xtc  
Gromacs trr format| trr| .trr  
HDF map| hdf|  
HSSP sequence| hssp| .hssp  
HTML| html| .html, .htm, .xhtml, .xht, .xml  
Image stack| images| .tif, .tiff, .png, .pgm  
IMAGIC density map| imagic| .hed, .img  
Imaris map| ims| .ims  
IMOD map| imodmap| .rec  
Integrative/Hybrid Models| ihm| .ihm  
MacMolPlt grid| macmolplt| .mmp  
Macromolecular Transmission| mmtf| .mmtf  
Marker model| markers| .cmm  
MOL/SDF| sdf| .sdf, .mol  
mmCIF| mmcif| .cif, .mmcif  
MRC density map| mrc| .mrc  
PIR sequence| pir| .ali, .pir  
NetCDF generic array| netcdf| .nc  
PDB| pdb| .pdb, .pdb1, .ent, .pqr  
Pfam sequence| pfam| .selex, .slx, .pfam  
Priism microscope image| priism| .xyzw, .xyzt  
PROFEC free energy grid| profec| .profec  
Interatomic pseudobonds| pseudobonds| .pb  
Purdue image format| pif| .pif  
Python code| python| .py  
Segger segmentation| segger| .seg  
SITUS map file| situs| .sit, .situs  
SPIDER volume data| spider| .spi, .vol  
STL (3D printing)| stl| .stl  
Stockholm sequence| stockholm| .sth, .sto  
STORM microscopy| storm| .storm  
Mol2| mol2| .mol2  
TOM toolbox EM density map| tom_em| .em  
Chimera BILD object| bild| .bild, .bld  
UHBD grid, binary| uhbd| .grd  
VTK PolyData| vtk| .vtk  
Wavefront OBJ| obj| .obj  
  
Database| Formats  
---|---  
ccd| ccd  
cellPACK| cellpack  
eds| ccp4  
edsdiff| ccp4  
emdb| ccp4  
pdb| mmcif, mmtf, pdb  
pdbdev| ihm  
pdbe| mmcif, pdb  
pdbj| mmcif, pdb  
pubchem| sdf  
smiles| smiles  
uniprot| uniprot  
  

> help help:user




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        4.0G         33G        250M         25G         57G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia

Change History (7)

comment:1 by Eric Pettersen, 5 years ago

Cc: Tom Goddard added
Component: Unassigned → MD/Ensemble Analysis
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Failure reading DCD: unexpected end of data

comment:2 by Eric Pettersen, 5 years ago

How did you concatenate the 9 DCD files together?

With the PDB reader skipping many ATOM records, it would seem unlikely that the final DCD will be usable with the PDB model.

At any rate, I am almost certain not to have time this week to investigate, though Tom might.

--Eric

in reply to:  3 ; comment:3 by Tristan Croll, 5 years ago 

"How did you concatenate the 9 DCD files together?"

I didn't - just tried to open the first. That's how it's typically done 
in e.g. VMD.

"With the PDB reader skipping many ATOM records, ..."

That wasn't the issue, I think. I ran a quick script to strip the TER 
lines out of the PDB before opening, and the result looked perfectly 
reasonable.


On 2020-05-18 17:21, ChimeraX wrote:

comment:4 by Eric Pettersen, 5 years ago

It depends. Was it one huge DCD file split into 9 chunks at arbitrary size boundaries, or was it 9 quasi-self-contained DCD files? ChimeraX would not handle the former.

in reply to:  5 ; comment:5 by Tristan Croll, 5 years ago 

I'm afraid I don't know the answer to that. It *did* open in VMD (had to 
download a copy... hasn't changed much), which got me what I needed (I 
only really wanted to compare the final frame to the first).

On 2020-05-18 17:38, ChimeraX wrote:

comment:6 by Eric Pettersen, 5 years ago

Okay, there must be a newer version of the DCD-reading library than what we have. From experience, that will likely be a pain to adapt.

comment:7 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

In the remarks section of the DCD, the parts past the null in the 80-character fields could contain garbage, so avoid trying to utf-8 decode them.

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