[Chimera-users] Chimera length units

Thomas Goddard goddard at cgl.ucsf.edu
Thu Nov 2 13:46:21 PST 2006

Hi Jeff,

  Chimera does not know what units you are using, the data coordinates
are just numbers as far as it is concerned.  If you open a PDB atomic
model the coordinates are always Angstroms.  If you open a density
map, say an MRC file, the header may include the voxel size.  That
value could be in Angstroms or nanometers.  Often maps don't have the
true voxel size in the header, often they say it is 1.  In such cases
you can use the Chimera volume dialog menu entry "Features / Origin and
Scale" to set the voxel size in Angstroms or nanometers so that the map
can be aligned with other models or maps.  If you open a PDB model in
Angstroms and a map with the scale set in nanometers then the map will
look 10 times smaller than it should be relative to the model.


> From: Jeff
> To: "'Thomas Goddard'" <goddard at cgl.ucsf.edu>
> Date: Thu, 2 Nov 2006 13:26:11 -0800
> thanks Tom,
> sorry for a goofy question, but how do I know what units chimera is using
> (for measuring distances, having the output is nice in Angstroms, but
> sometimes (like with orienting a clipping plane) using unitless/pixels is
> more handy for displacements/etc)
> thanks,
> -jeff

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