[Chimera-users] Chimera memory management

Thomas Goddard goddard at cgl.ucsf.edu
Tue Jan 31 11:04:31 PST 2006

Hi Mike,

  Are you running out of memory loading molecular models (PDB files)
or volume data?  If volume data, what file format?  How much memory
does your machine have?  What operating system are you running
(Windows, Mac, Linux)?

  I guess from your error message you are reading volume data.  Chimera
will by default read in the entire volume.  If you look at the file size
you can see how big that is.  In versions of Chimera older than 1.2143
(June 25, 2005) two copies of the volume were in memory when reading
the file.  The more recent versions only put one copy in memory.

  If the file is simply too big to read the whole thing in then you
can change some settings in the Volume Viewer dialog and read in only
part of the data set.  For some file formats this will not help because
the whole data set is read in even if only a piece of the data is requested
(eg. DSN6, Delphi, XPLOR).  Other formats will read only the part of the
data you request (eg. MRC / CCP4).  In Chimera 1.2184 or newer use menu entry

	Tools / Volume Data / Volume Viewer

and then use volume dialog menu entry

	Features / Data Display Options

This shows a setting in the volume dialog that says "Show data when opened
if smaller than 256 Mvoxels".  Change the 256 to a smaller number so that
your file does not get immediately read when opened, or click off the switch
so no volume data will be read immediately on opening.  Then open your
volume data with Chimera menu entry File / Open....  The data will not be
shown.  Use volume dialog menu entry

	Features / Region bounds

You will see in the volume dialog a line like

	Region min max step   x 0 255 1   y 0 255 1   z 0 255 1

In this example the data set is 256 by 256 by 256.  To display just a
128 ^ 3 subblock starting at index 0,0,0 I would change these numbers to:

	Region min max step   x 0 127 1   y 0 127 1   z 0 127 1

Then press the volume dialog Show button.

  These features are described in the Chimera User's Guide under the
Tools section, under Volume Viewer.  You can press the Help button on the
volume dialog to see that documentation.


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