[Chimera-users] density maps in chimera- question

Thomas Goddard goddard at cgl.ucsf.edu
Thu Aug 21 15:49:50 PDT 2008

Hi Sarah,

   You can use the keyboard shortcut "bv" to create a new map that 
covers your PDB model.  To enable keyboard shortcuts use Tools / General 
Controls / Keyboard Shortcuts and turn on "Enable keyboard shortcuts" in 
the dialog.  Select the atoms of your PDB model.  If you have more than 
one map open make sure the highlighted one in the volume dialog is the 
crystal map for the selected atoms.  Then type the "bv" shortcut to 
create a new map covering the select atoms.  This assumes that the 
starting map is a full unit cell.  If you don't want to go to the 
trouble of enabling keyboard shortcuts, you can use the command "ac bv" 
which runs the shortcut (accelerator) bv.  You can save the covering map 
with volume dialog File / Save Map As....


Sarah Boyce wrote:
> Hi Tom- I was told you might be the person to ask about the density map 
> features in chimera. I'm trying to display crystallographic electron 
> density maps and I've run into a problem aligning some of the maps to 
> the protein model. When I load the map and model it looks as though the 
> map is of the symmetry related molecule, but when viewed using Coot it 
> automatically centers the map on the model. So far the only tool that 
> I've found to do this is by hand alignment, which doesn't work at all 
> for an atomic level model (or at least when I've tried it it is too much 
> of a pain). Is there an automated tool in chimera that will 
> automatically center the map on the model similar to the way Coot 
> handles it?
> Thanks, Sarah

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