In Chimera “atoms” means an atomic model, for example from a PDB file, not a density map. If you want to reduce your map to a cube by cropping and it is size 54,36,51 use command
volume #0 region 0,0,0,35,35,35
That gets the lower left corner. To get the center part
volume #0 region 9,0,7,44,35,42
The 6 numbers are imin,jmin,kmin,imax,jmax,kmax where i,j,k are indices along the 3 map axes. You can also do this with the Volume Viewer dialog menu entry Features / Region Bounds, or interactively with the mouse using Features / Subregion Selection. For more info about map manipulations
Tom
On Apr 15, 2015, at 1:17 PM, Sushree Tripathy wrote:
Hi,
Thanks for your prompt reply. What I am trying to do is I have a map which I have loaded in chimera as #0. Now I want to reduce it to cubic size. Since the syntax is "
vop boxes volume-spec atom-spec size d", so I am choosing #0 for my volume and all the atoms in that volume. so #0 again. Please correct me if I am wrong.
Thanks
Sushree.