[Chimera-users] Cubic vop zone boxes

Morris, Kyle Kyle.Morris at warwick.ac.uk
Tue Dec 8 02:23:19 PST 2015

Thanks Tom, this is perfect, I hadn’t figured it out with vop cover, this is a perfect example to get going!


On 7 Dec 2015, at 19:59, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

Hi Kyle,

  So you want to extract a cube shaped region of a density map containing a PDB model.  If you are using vop zone then the values are set to zero outside the zone distance.  Using the “minimalBounds” option you get a rectangular box instead of a cube.  From that non-cube box you want to extend the two shorter dimensions to equal the size (in grid points) of the longest of the x,y,z dimensions?  That may involve extending beyond the bounds of the original map.  The “vop cover” command can almost do what you want.  It extends a map, mostly for handling unit cell and crystal symmetries, but you can turn off the symmetry handling.  So if you have an extracted rectangular map of size (96, 101, 88) and you want make it size (101,101,101) with zero padding, the following command does this

vop cover #0 ibox -2,0,-6,98,100,94 useSymmetry false cellSize 200,200,200

documentation here


The trouble is that the integers you need to use depend on the original rectangular size.  I’ve attached a Python script cube.py that will do this — you would run it as a Chimera command like

run /tmp/cube.py #0

and it will in turn run the appropriate vop cover command.



On Dec 7, 2015, at 8:11 AM, Morris, Kyle wrote:

Hi Chimera team and users,

I am cutting out multiple sub-volumes from a much larger volume (#0) with fitted PDB co-ordinates (#1-n) using a script, but having trouble making the final sub-volumes cubic. At present I am using cutting out sub-volumes using '$ vop zone #0 #1 10 minimalBounds true’ to make the sub-volume more manageable.

I am aware of the previous questions posted at http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-April/010942.html for reducing a volume size and the trick at http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006208.html for expanding a volume.

Is there however a way to make the volume cubic at the vop zone stage or a one liner command to expand a box after cutting with minimalBounds so that this can be efficiently scripted?

Thanks for your help!
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