id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2737 Normals reversed for negative contours Tristan Croll Tom Goddard "{{{ 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: 0.91 (2019-12-23) Description When displaying a volume surface in wireframe representation, negative contours appear to have their normals reversed (what is light should be dark and vice versa). The red surface in the attached image is an example (the -3 sigma Fo-Fc contour in a crystallographic map). Solid/transparent surfaces seem fine. A related question: is it possible to have the option to exclude wireframe surfaces from directional lighting entirely, so they're only affected by the depth cueing fog? Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open LTA-R3_refine_14.pdb Summary of feedback from opening LTA-R3_refine_14.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-01-10 Time 18:35:56 GMT +0000 (1578681356.67 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/review/2020_burmeister/revised_model/LTA-R3.mtz 48 messages similar to the above omitted Chain information for LTA-R3_refine_14.pdb #1 --- Chain | Description A B | No description available X | No description available Y | No description available > open LTA-R3_refine_14.pdb Summary of feedback from opening LTA-R3_refine_14.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-01-10 Time 18:35:56 GMT +0000 (1578681356.67 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/review/2020_burmeister/revised_model/LTA-R3.mtz 48 messages similar to the above omitted Chain information for LTA-R3_refine_14.pdb #2 --- Chain | Description A B | No description available X | No description available Y | No description available > matchmaker #2/B to #1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker LTA-R3_refine_14.pdb, chain A (#1) with LTA-R3_refine_14.pdb, chain B (#2), sequence alignment score = 1890.7 RMSD between 361 pruned atom pairs is 0.480 angstroms; (across all 362 pairs: 0.496) > ~cartoon #2/A > hide #2 > hide > ~cartoon #1/B > show #1/A > show #2/B > show nucleic > usage matchmaker matchmaker matchAtoms to an atoms specifier [pairing a text string] [alg a text string] [verbose true or false] [ssFraction ssFraction] [matrix a text string] [gapOpen a number] [hgap a number] [sgap a number] [ogap a number] [cutoffDistance cutoffDistance] [gapExtend a number] [bring a models specifier] [showAlignment true or false] [computeSs true or false] [matHh a number] [matSs a number] [matOo a number] [matHs a number] [matHo a number] [matSo a number] — Align atomic structures using sequence alignment ssFraction: a number or true or false cutoffDistance: a number or none > 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"") > select #1/A 2962 atoms, 3021 bonds, 6 pseudobonds, 2 models selected > select #1/A&protein 2933 atoms, 2992 bonds, 1 model selected > select #2/B&protein 2933 atoms, 2992 bonds, 1 model selected > isolde start > set selectionWidth 4 Chain information for LTA-R3_refine_14.pdb --- Chain | Description 1.1/A 1.1/B | No description available 1.1/X | No description available 1.1/Y | No description available Done loading forcefield > close #1.2-3#2#1.1 > open 3io0 structureFactors true Summary of feedback from opening 3io0 fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma, pdbx_anom_difference, pdbx_anom_difference_sigma, intensity_meas, intensity_sigma, pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma Automatically choosing ""intensity_meas, intensity_sigma"". notes | Resolution: 3.003 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 --- Chain | Description 2.1/A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > close #1 > clipper spotlight radius 13.00 > clipper spotlight radius 14.00 > clipper spotlight radius 15.00 > clipper spotlight radius 16.00 > clipper spotlight radius 17.00 > clipper spotlight radius 18.00 > clipper spotlight radius 19.00 > clipper spotlight radius 20.00 > clipper spotlight radius 21.00 > clipper spotlight radius 22.00 > clipper spotlight radius 21.00 > clipper spotlight radius 20.00 > clipper spotlight radius 19.00 > clipper spotlight radius 18.00 > clipper spotlight radius 17.00 > clipper spotlight radius 16.00 > clipper spotlight radius 15.00 > clipper spotlight radius 14.00 > clipper spotlight radius 20 > clipper spotlight radius 15 > hide #2.3 models > show #2.3 models > hide #2.3 models > show #2.3 models > hide #2.3 models > show #2.3 models > set bgColor white > set bgColor black > set bgColor white > set bgColor black > hide #!2.2.1.2 models > show #!2.2.1.2 models > hide #!2.2.1.4 models > select clear > select clear > color bychain > color bychain > color byhetero > color bfactor 1658 atoms, 230 residues, atom bfactor range 27.5 to 73.7 > color bychain > color byhetero > color byattribute occ No known/registered attribute occ > color byattribute occupancy #1 No atoms specified > color byattribute occupancy #2 1658 atoms, 230 residues, atom occupancy range 1 to 1 > set bgColor white QWidget::repaint: Recursive repaint detected > color bychain > color byhetero > set bgColor black > select clear > select clear > save /home/tic20/Desktop/wireframe_lighting.jpg > show #!2.2.1.4 models OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: wireframe_lighting.jpg }}} [attachment:""wireframe_lighting.jpg""] " defect closed normal Volume Data not a bug all ChimeraX