[Chimera-users] suggested improvements

Dougherty, Matthew T matthewd at bcm.edu
Mon Jun 30 15:54:53 PDT 2014

1) first suggestion

on the sym command the following is defined

icosahedral symmetry I[,orientation] around center

    Example: i,n25 

where orientation can be:

    222 (default) - with two-fold symmetry axes along the X, Y, and Z axes
    2n5 - with two-fold symmetry along X and 5-fold along Z
    n25 - with two-fold symmetry along Y and 5-fold along Z
    2n3 - with two-fold symmetry along X and 3-fold along Z
    222r - same as 222 except rotated 90° about Z
    2n5r - same as 2n5 except rotated 180° about Y
    n25r - same as n25 except rotated 180° about X
    2n3r - same as 2n3 except rotated 180° about Y 

In the chimera tool->higher order structure -> the icosahedral structure 
it defines similar orientations, assume in the same order.

It would be helpful on the selections to include the sym syntax as part of the icosahedral structure text
ie {222} xyz 2 fold
   {2n5} x 2 fold z 5 fold

2) second suggestion
When reading an MRC file I occasionally see situations that make me question whether the file is EMDB complaint. 

It would be good to have the means to dump the MRC header, even if chimera refuses to read the file in its entirety. 

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine

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