[Chimera-users] viewing grid density

Thomas Goddard goddard at cgl.ucsf.edu
Thu Oct 26 10:11:51 PDT 2006

Hi Bala,

  Elaine Meng answered these questions before I finished my email.
I think my answers are the same, but I'll give them to you anyways.

  If the solvent map and reference PDB structure produced by Amber8 do
not align when displayed in Chimera that is probably a problem with
Amber or how you are using Amber.  If they do not align I do not think
you will be able to align them in Chimera.  The one thing you could
try is to use volume dialog menu entry Features / Origin and Scale.
That will show the grid plane spacing (called "voxel size") and the
origin that is being used for the map.  You can try changing those
values by hand.  Press the Enter key after changing a value to have
the display updated.

  Chimera can compute solvent occupancy from a trajectory using its
MD Movie tool.  See the "occupancy analysis" section of the Chimera


Perhaps this is an alternative way to do what you want.

  The threshold level in the Chimera volume dialog specifies what map
value the contour surface is drawn at.  The displayed surface goes
through those points in space where the map has the specified value.
What that means depends on what the values in your map mean.  I don't
know what the values in your solvent map computed by Amber8 mean.

  Here is the Chimera users list (found under the Contact Us link on
the main Chimera web page):



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