[Chimera-users] "newmap" command? (Or other way to resample on arbitrary grid?)

Tom Goddard goddard at sonic.net
Tue Jul 28 14:26:40 PDT 2015


Hi Oliver,

 You can resample a map with a different grid spacing using the Volume Viewer dialog menu Features / Subregion Selection, enable “Rotate selection box, sample at voxel size S”,
set the voxel size to the grid spacing you want, middle click outside the volume to show a box around the entire map, then press Crop.

 Unfortunately the "vop resample” command won’t do this.  The natural way would be to specify a non-integer value for the gridStep parameter, but it won’t accept that.  I looked at the code and it would require too many changes with too big a chance of breaking other code to quickly add that.  So it won’t happen until Chimera 2.

	Tom


> On Jul 28, 2015, at 8:26 AM, Oliver Clarke wrote:
> 
> Hi all,
> 
> Is there any way to use vop to resample on an arbitrary grid, that is, not the grid of an existing map? This would be useful, for example, when one wants to interpolate to finer grid spacing than is present in the input map (but otherwise keeping the original dimensions and origin).
> 
> I note in the old chimera documentation that there used to be a command called “newmap” (http://www.cgl.ucsf.edu/chimera/experimental/resample_map/resamplemap.html) which allowed for the generation of an arbitrary map which one could use for exactly this purpose, but this command does not seem to be recognized by modern Chimera builds. Does this command still exist somewhere under a different name? Or is there another way to accomplish this?
> 
> Cheers,
> Oliver.
> 



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