Name

sxrot_sym - find 3D rotation that will place the volume in agreement with a specified point-group symmetry

Usage

Usage in command lines:

sxrot_sym.py input_filename output_filename --sym=Symmetry group --phi --theta --psi=The 3 Eulerian angles in degrees --r=Radius of mask --phirange --thetarange --psirange=A search scale for each angle --ftol --xtol = convergence criterion the function and angles values

Usage in python programming:

rot_sym(infile, outfile, sym_gp="d4", radius=None, phi=0, theta=0, psi=0, phirange=20, thetarange=20, psirange=20, ftolerance=1.e-4, xtolerance=1.e-4)

Input

infilename

The filename of the volume to be rotated and symmetrized using the specified point-group symmetry. The filename should be given within double quotes with file extension (eg:"in.spi").

Output

outfilename

The name of the output file where the rotated and symmetrized volume is stored. The filename should be given within double quotes with file extension (eg: "out.spi").

Options

--sym

string that specifies the point-group symmetry: for example "c3", or "d4", or "icos". To copy the volume, use "c1". (default="c1")

--phi

phi angle in degrees. (default:0)

--theta

theta angle in degrees. (default:0)

--psi

psi angle in degrees. (default:0)

--r

The radius of mask. (default: None)

--phirange

The search scale for phi angle...(default = 20.). Remember that value should be > 0

--thetarange

The search scale for theta angle...(default = 20.). Remember that value should be > 0

--psirange

The search scale for psi angle...(default = 20.). Remember that value should be > 0

--ftol

Convergence criterion on the function values (default = 1.e-4)

--xtol

Convergence criterion on the variable(angles) values (default = 1.e-4)

Description

• The command rotates and symmetrizes the volume specified in the infilename.
• The final volume is saved in outfilename.
• It is advisable to give a good initial guess on the angles [phi,theta,psi].
• The scale,ftol and xtol could be used to make the search faster.

Author / Maintainer

Bharath K Narayanan

Keywords

category 1

APPLICATIONS

Files

applications.py,sxrot_sym.py

Maturity

stable

works for most people, has been tested.

Bugs

None. It is perfect.