id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2556 DICOM reader: broken data stream when reading image file satyshur@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.1.1.el7.x86_64-x86_64-with-redhat-7.7-Maipo ChimeraX Version: 0.91 (2019-09-30) Description Reading DICOM directory Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-09-30) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/satyshur/superoxide-dismutase/SodCII_refine_21-coot-3_zanuda1.pdb Summary of feedback from opening /home/satyshur/superoxide- dismutase/SodCII_refine_21-coot-3_zanuda1.pdb --- warning | Ignored bad PDB record found on line 1 REMARK subgroup_number 1 Chain information for SodCII_refine_21-coot-3_zanuda1.pdb #1 --- Chain | Description A B C D E F G H | No description available > style stick Changed 8240 atom styles > style ball Changed 8240 atom styles > view > view cofr false > lighting full > lighting soft > lighting simple > style stick Changed 8240 atom styles > style sphere Changed 8240 atom styles > color byhetero > color bychain > color byhetero > rainbow > color bfactor 8240 atoms, 1144 residues, atom bfactor range 2.4 to 48.1 > rainbow > mlp Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_A SES surface"": minimum -27.06, mean -6.296, maximum 19.96 Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_B SES surface"": minimum -28.6, mean -6.484, maximum 22.4 Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_C SES surface"": minimum -27.3, mean -6.31, maximum 19.34 Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_D SES surface"": minimum -28.35, mean -6.47, maximum 21.23 Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_E SES surface"": minimum -30.86, mean -6.3, maximum 19.5 Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_F SES surface"": minimum -27.09, mean -6.42, maximum 21.37 Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_G SES surface"": minimum -30.58, mean -6.366, maximum 19.85 Map values for surface ""SodCII_refine_21-coot-3_zanuda1.pdb_H SES surface"": minimum -27.33, mean -6.48, maximum 20.92 > color bfactor 8240 atoms, 1144 residues, 8 surfaces, atom bfactor range 2.4 to 48.1 > color bychain > color byhetero > color bynucleotide > hbonds 743 hydrogen bonds found > interfaces ~solvent 8 buried areas: H G 757, E F 753, A B 713, C D 708, A H 480, C F 476, D E 471, B G 464 /opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/networkx/drawing/nx_pylab.py:579: MatplotlibDeprecationWarning: The iterable function was deprecated in Matplotlib 3.1 and will be removed in 3.3. Use np.iterable instead. if not cb.iterable(width): > show surfaces > hide surfaces > show surfaces > show cartoons > hide cartoons > show cartoons > hide surfaces > hide cartoons > show cartoons > show atoms > hide cartoons > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting soft > lighting full > lighting simple > lighting soft > lighting full > open /home/satyshur/Downloads/dicom format dicom Summary of feedback from opening /home/satyshur/Downloads/dicom --- warnings | Missing PixelSpacing, using value 1, /home/satyshur/Downloads/dicom/bmode.dcm Cannot determine z spacing, missing ImagePositionPatient, using value 1, /home/satyshur/Downloads/dicom/bmode.dcm broken data stream when reading image file Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3568, in _update_drawings v.update_drawings() File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/volume.py"", line 715, in update_drawings self._keep_displayed_data = self.displayed_matrices() File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1628, in displayed_matrices matrices.append(self.matrix(read_matrix)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1143, in matrix m = self.region_matrix(r, read_matrix) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/volume.py"", line 1167, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/map/data/griddata.py"", line 249, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/dicom/dicom_grid.py"", line 146, in dicom_read_matrix self.time, c, m, progress) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/dicom/dicom_format.py"", line 522, in read_matrix a = self.read_frames(time, channel) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/dicom/dicom_format.py"", line 567, in read_frames data = d.pixel_array File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/pydicom/dataset.py"", line 1362, in pixel_array self.convert_pixel_data() File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/pydicom/dataset.py"", line 1308, in convert_pixel_data raise last_exception File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/pydicom/dataset.py"", line 1276, in convert_pixel_data arr = handler.get_pixeldata(self) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/pydicom/pixel_data_handlers/pillow_handler.py"", line 188, in get_pixeldata UncompressedPixelData.extend(decompressed_image.tobytes()) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PIL/Image.py"", line 762, in tobytes self.load() File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PIL/ImageFile.py"", line 272, in load raise_ioerror(err_code) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PIL/ImageFile.py"", line 58, in raise_ioerror raise IOError(message + "" when reading image file"") OSError: broken data stream when reading image file Error processing trigger ""graphics update"": OSError: broken data stream when reading image file File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PIL/ImageFile.py"", line 58, in raise_ioerror raise IOError(message + "" when reading image file"") See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 340.107 OpenGL renderer: Quadro FX 4800/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Input/Output nonchimerax all ChimeraX