[Chimera-users] delphi potenital map viewing

Thomas Goddard goddard at cgl.ucsf.edu
Thu Dec 4 15:23:15 PST 2003

Hi Klaas,

  The size of the Delphi potential map Chimera can display is only
limited by the size of your computer memory.

  If you open a large map it does not get shown immediately if the map
is larger than 1 Mvoxels (~100^3).  This is controlled by an option
under the Volume Viewer options pane "Show data when opened if smaller
than XXX Mvoxels".  If you open a large data set, you need to press
the Show button at the bottom of the Volume Viewer dialog to display
it.  This is intended to allow you to adjust the bounds to show a
subregion and avoid loading the whole map.  This setting can be
changed to specify a larger volume limit, or always show the data
immediately when opened.

  When you press Show to display the large map, it will show a
subsampled version, for example skipping every other plane along
each axis.  This is indicated in the "Step" menu near the top of
the Volume Viewer dialog.  The automatic subsampling happens because
of another Volume Viewer / Options setting "Adjust step to show at
most XXX MVoxels".  The default setting is to subsample for data
sets larger than 2 MVoxels.  You can change the step to not do
subsampling using the Step menu (set it to "1 1 1").  You can turn
off the automatic subsampling option or increase the volume size

  Delphi grid values are 4 byte floats, so a 213^3 map will take
about 38 Mb (213^3 * 4), plus some additional memory will be used
to make a surface representation.  I've worked with 256^3 maps with
no problem.  Probably the practical limit is around 512^3 for a
machine with a gigabyte of memory.


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