Misalignment of lines and glyphs in alignment annotation

When an EPS alignment figure using the example alignment is viewed close up, two problems can be seen:
 The corners of Lines surrounding region definitions are not properly aligned - probably due to rounding errors.
 The central axis of the secondary structure element glyphs are not aligned with the grey coil line.

See the attached image.

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This is either a rounding error or a simple mis-calculation in the rendering routines. Very easy to fix.