id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2758	Place.rotation_axis_and_angle not robust	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 (2020-01-11)
Description
Place.rotation_axis_and_angle() returns incorrect values when the rotation matrix is symmetric or nearly so. Following the link to http://en.wikipedia.org/wiki/Rotation_matrix from core.geometry.matrix.R_to_axis_angle():

""This does not work if R is symmetric. Above, if R − R T  is zero, then all subsequent steps are invalid. In this case, it is necessary to diagonalize and find the eigenvector corresponding to an eigenvalue of 1. ""

Simple case of a flip about x:
{{{
p = Place(axes=[[1,0,0],[0,-1,0],[0,0,-1]])

p.rotation_axis_and_angle()
(array([0., 0., 1.]), 0) # should be [1,0,0],180

# A more ""real"" case with some numeric noise

p = Place(axes=[[1,0,0],[-1e-16,-1,0],[-1e-16,0,-1]])

p.rotation_axis_and_angle()
(array([ 0.        , -0.70710678,  0.70710678]), 180.0)

}}}

Log:
UCSF ChimeraX version: 0.92 (2020-01-11)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6ig2 structureFactors true

Summary of feedback from opening 6ig2 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
intensity_meas, intensity_sigma  
Automatically choosing ""intensity_meas, intensity_sigma"".  
notes | Fetching compressed mmCIF 6ig2 from
http://files.rcsb.org/download/6ig2.cif  
Fetching CCD CTP from http://ligand-expo.rcsb.org/reports/C/CTP/CTP.cif  
Fetching compressed 6ig2 structure factors from
http://files.rcsb.org/download/6ig2-sf.cif  
Resolution: 2.8817619976202815  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
6ig2 title:  
Structure of mitochondrial CDP-DAG synthase Tam41 complexed with CTP, δ 74,
F240A [more info...]  
  
Chain information for 6ig2  
---  
Chain | Description  
1.1/A 1.1/B 1.1/C 1.1/D | Phosphatidate cytidylyltransferase, mitochondrial  
  
Non-standard residues in 6ig2 #1.1  
---  
CTP — cytidine-5'-triphosphate  
  
6ig2 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> 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"")  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

}}}
"	defect	closed	normal		Core		fixed						all	ChimeraX