Symmetrize

• Description
• Description of Inputs
• Command Procedures
• Update History
• Bugs and Warnings

Description

Symmetrize uses a two-fold map of the sort produced by emicofb or the two fold map in the 222 orientation. It allows production of maps in arbitrary orientations and to any scale. Varying amounts of symmetry can be applied including N fold rotational symmetry.

Inputs

• Prompts are displayed along with the standard icosahedral inputs are indicated with >'s and italics.

  ---

  Selection of symmetry matrices 
     Full icos           - I 
     3 lacking from D5   - D 
     All threes          - 3 
     All fives           - 5 
     All twos            - 2 
     N fold along Z      - Z 
     identity            - 1 
     invert hand         - H
     XYZ 2f              - P 
     icos 1-5            - F 
     icos 1-20           - T 
     Step by step        - ? 
  

• > d (since 52 symmetry has already been applied)

  Transformation of symmetry matrices 
  Input orientation 
  The standard icosahedral matrices are based 
    on a setting in which the two fold axes are 
    are assumed to lie on X,Y,Z. 
  Is this true in the map  (Y or N) ? 
  

• > n (since the input map from FB is not 222

  The 52 setting is assumed (ie the FB setting).
  Two fold axis along Z (slow)
  Place 5 fold along Y (medium) 
  .
  .
  .
  .
  Default output map will be in orientation 
    where one two fold is along z and one five fold 
     is along y 
   Is this the desired orientation (Y or N)?
  

• > n (this allows selection of another orientation than the input)

   Do you want Crowther 222 viewed down z,  view down 2f(25),3f,5f axis  or general view (c,2,3,5,g)?
  

• > 3 (Rotates map so that output map is viewed with the icosahedral three fold along Z)

  Enter name of MRC format density file  (A80) 
  

• > lpro_test_2f.mrc

  Size of output maps ROW,COL,SEC (3i  gives input values) 
  

• > 200,200,200 (input map was 100,100,100 so this would be magnification)

  This yields a scale of    0.50000     relative to the original map 
  input new scale (out_pixel=in_pixel/scale) 
   or  if this scale is correct 
  

• > 0.75 (this would produce a map with 0.75 of the original map units per output map unit - so the 100**3 map would fill 150**3 output map units)

  DENSITY_SCALE - scale factor for density (  gives 1.0) 
  

• > -1.0 (this would reverse the sign of the map)

   Radial crop - min and max radius for orig map
   (  gives)   0.0000000E+00 ,    46.00000    
  

• > 10.,45., (this would only leave the portion of the density between radius 10 and radius 45 in the original map or 15 and 135 in the output map )

  Enter name of output MRC file  (A80) for  averaged map
  

• > lpro_test_2fsym.mrc

  Enter name of output MRC file  (A80) for  standard deviation map 
  

• > lpro_test_2fsym_stdev.mrc (if the standard deviation map is not desired one can use the null device for this file)

Sample runs

Update History

Current version - 25jul95

hand changes - 25jul95

added option to allow the change of hand by reflecting the Z axis - sdf

Speed Up - 16oct95 - sdf

A new version which uses BLAS routines for the most computationally intensive portion of the calculation is now functional. The speedup is 4 to 5 fold on large (>128^3) maps and somewhat more on smaller ones.

Author: Stephen Fuller

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Last Updated: October 16'th 1995