[Chimera-users] Question from PhD student

Tom Goddard goddard at sonic.net
Thu Jan 28 12:33:47 PST 2016

Hi T.I,

  The “vop boxes” command is intended to do this but ends of giving box dimensions that differ by 1 grid point (like 149 by 149 by 150).  A few other people have asked about this recently.  So I’ve fixed vop boxes in tonight’s Chimera daily build so you can say

	vop boxes #0 #1 isize 150

where #0 is the density map and #1 are the markers and “isize 150” means extract a map for each marker that is 150 by 150 by 150 grid points.  This “isize” option is new.  The previous option “size” still exists but is specified in Angstroms.  If you use that option it will also give cubes, but depending on where the marker is centered between grid points, the cube sizes could differ by 1 grid point for different markers.  So I added the isize option so you could get exactly the same number of grid points for each marker.  This isn’t exactly true — you don’t always get cubes — if the marker is too close to the edge of the density map so the box would go outside the map, then the extracted region is not a cube.  Would be nice if it could fill it with zeros and make it a cube but it doesn’t do this now.


> On Jan 28, 2016, at 10:09 AM, T-I <ignatiou at gmail.com> wrote:
> Dear Chimera,
> I would like to know exactly how to enclose my EM density map within a cube of specified size (where x, y and z have equal dimensions,       i.e  x,y,z = 150 pixels).
> It seems that when I place a marker (from volume tracer) on my map and then specify the padding number a rectangular cube is produced instead.
> I there a simple command to do this or can it be done from the GUI?
> Many thanks
> T.I
> PhD student, London
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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