[Chimera-users] Chimera length units

Thomas Goddard goddard at cgl.ucsf.edu
Thu Nov 2 16:05:50 PST 2006

Hi Jeff,

  Chimera clipping and other tools use xyz coordinates and do not use
voxel or pixel measures.  The volume dialog region bounds panel and
the volume dialog step size are exceptions where voxel index positions
are used.

  The notion of a voxel is only relevant to density maps, not atomic
models and clippping applies to all kinds of data, not just maps.

  Screen pixels are a 2 dimensional concept so it is an awkward
measure to use especially with perspective 3-d viewing for measuring


> From: Jeff
> To: "'Thomas Goddard'" <goddard at cgl.ucsf.edu>
> Subject: RE: Chimera length units
> Date: Thu, 2 Nov 2006 14:30:30 -0800
> does this mean that I can't refer to a given coordinate by pixel/voxel
> location without resetting the voxel size to '1 1 1' (which I might not want
> to do - does chimera not keep the mrc file (or other voxel data) inside of a
> similar kind of array) 
> > -----Original Message-----
> > From: Thomas Goddard [mailto:goddard at cgl.ucsf.edu] 
> > Sent: Thursday, November 02, 2006 1:46 PM
> > Cc: chimera-users at cgl.ucsf.edu
> > Subject: Chimera length units
> > 
> > 
> > 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.
> > 
> > 	Tom

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