id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2799 Normals parellel to Z axis inverted 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: 0.92 (2020-02-03) Description If I use the below code to generate a set of dashed lines (representing symmetry axes in a crystal), the normals come out reversed for about half of them. Probably not coincidentally, all the offenders I see are exactly parallel to the Z axis. Looks like in this case `geometry.cylinder_rotations()` can return a reflection operator with all diagonal elements negative (when z0 is greater than z1?). Example `Places` array pasted below. I've confirmed that flipping the offending diagonals back to positive values fixes the display. {{{ def sym_axis_drawing_screw(fold_symmetry, screw_component, axyz0, axyz1, base_radius=0.3): ''' Just draw as a dashed cylinder for now. ''' import numpy from chimerax.surface.shapes import dashed_cylinder_geometry from chimerax.core.geometry import Places, cylinder_rotations, rotation n = len(axyz0) radius = base_radius*(1+0.1*fold_symmetry) radii = numpy.ones(n, numpy.float32)*radius rot44 = numpy.empty([n,4,4], numpy.float32) cylinder_rotations(axyz0, axyz1, radii, rot44) rot44[:,3,:3] = 0.5*(axyz0+axyz1) from chimerax.core.graphics import Drawing d = Drawing('{}-fold screw axis'.format(fold_symmetry)) d.set_geometry(*dashed_cylinder_geometry(segments=15)) d.color = _symmetry_colors[fold_symmetry][1] d.positions = Places(opengl_array=rot44) return d }}} {{{ fourfold.positions.array() Out[30]: array([[[ 4.200e-01, -0.000e+00, 0.000e+00, -3.574e+01], [-0.000e+00, 4.200e-01, 2.424e-14, -1.212e-14], [-0.000e+00, -6.754e-17, 1.507e+02, -7.535e+01]], [[ 4.200e-01, -0.000e+00, 9.228e-15, -6.803e-15], [-0.000e+00, 4.200e-01, 0.000e+00, -3.574e+01], [-2.572e-17, -0.000e+00, 1.507e+02, -7.535e+01]], [[-4.200e-01, -0.000e+00, 0.000e+00, -7.148e+01], [-0.000e+00, -4.200e-01, 0.000e+00, -3.574e+01], [-0.000e+00, -0.000e+00, -1.507e+02, -7.535e+01]], [[-4.200e-01, -0.000e+00, 0.000e+00, -3.574e+01], [-0.000e+00, -4.200e-01, 0.000e+00, -7.148e+01], [-0.000e+00, -0.000e+00, -1.507e+02, -7.535e+01]]]) }}} Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.92 (2020-02-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6h0w format mmCIF fromDatabase pdb structureFactors true Summary of feedback from opening 6h0w 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 Automatically choosing ""F_meas_au, F_meas_sigma_au"". notes | Resolution: 1.2303244209351512 6h0w title: Crystal Structure of KDM4D with tetrazolylhydrazide ligand NS035 [more info...] Chain information for 6h0w --- Chain | Description 1.1/A | Lysine-specific demethylase 4D Non-standard residues in 6h0w #1.1 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) FHW — (2~{R})-3-phenyl-2-(2~{H}-1,2,3,4-tetrazol-5-yl)propanehydrazide I1L — [2-(2~{H}-1,2,3,4-tetrazol-5-yl)ethanoylamino]azanium NA — sodium ion NI — nickel (II) ion SO4 — sulfate ion ZN — zinc ion > toolshed show Shell /opt/UCSF/ChimeraX-daily/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"") > set bgColor white > set bgColor black > save /home/tic20/Desktop/wrong_normals.jpg > close #1.4 OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Graphics fixed all ChimeraX