[Chimera-users] fitting a protein inside an EM reconstruction

Thomas Goddard goddard at cgl.ucsf.edu
Fri Oct 6 10:33:04 PDT 2006

Hi Jayant,

  The problem with the EM map being too small for the crystal model is
that the SPIDER map header does not say the grid plane spacing.  Chimera
is giving it a default grid plane spacing of 1 angstrom.  To fix this
you need to know the grid plane spacing, also called "voxel size" in
Angstroms.  Then enter this value in volume dialog, using volume dialog
menu entry Features / Origigin and Scale.  Probably the plane spacing is
the same along the x, y and z axes, so you will enter the same number in
the 3 voxel size fields, and press the Return key to then have the map
displayed at the new scale.

  Unfortunately the above change does not modify your SPIDER file so it
will still have the wrong scale the next time you open it in Chimera.
Two solutions are to write the SPIDER map out in MRC format using the
volume dialog menu entry File / Save As, or save a Chimera session using
the main Chimera window menu entry File / Save Session As.  Chimera is
not able to write out new SPIDER format maps.


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