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

http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html

  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.

Sushree Tripathy
Graduate Student
Department of Physics
University at Buffalo

On Wed, Apr 15, 2015 at 4:13 PM, Tom Goddard wrote:
Hi Sushree,

  Why does your "vop boxes” command use model #0 for both the map and the markers?  That can’t be right.  If your marker(s) are in model #1 you would need “vop boxes #0 #1 size 36”.  What are you trying to do?


  Tom



On Apr 15, 2015, at 1:03 PM, Sushree Tripathy wrote:

Hi,

I went through the chimera user's guide and as per the syntax used  "vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" (the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map.

Please help.
Thanks
Sushree.

Sushree Tripathy
Graduate Student
Department of Physics
University at Buffalo
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