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 lengths. Tom

From: Jeff To: "'Thomas Goddard'" <goddard@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)

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-----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Thursday, November 02, 2006 1:46 PM Cc: chimera-users@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