[Chimera-users] Mirrored density artefact

Tom Goddard goddard at sonic.net
Thu Apr 7 19:56:57 PDT 2016


Hi Kyle,

  The vop cover command applies crystal symmetry to the map to cover the specified set of atoms.  I’m guessing your map is not an x-ray map, but this command assumes that it is the unit-cell of an x-ray map so it will tile space with copies of the volume box.  To avoid this problem add the “cellSize” option using very large values, for example,

	vop cover #0 atomBox #1 pad 55 cellSize 10000,10000,10000

This “vop cover" behavior is explained in the Chimera documentation

   https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover

 Tom


> On Mar 24, 2016, at 3:51 PM, Morris, Kyle wrote:
> 
> Dear Chimera dev and community,
> 
> I am using "vop cover” to extract a box of density around a PDB and making the box quite large with the following:
> 
> 	$ vop cover #0 atomBox #1 pad 55
> 
> I have noticed in the extracted density that as I increase the pad size the true density gets duplicated and mirrored on the opposite edge of the cell containing the volume. This seems like strange behaviour to me, is there something wrong or that I am doing wrong?
> 
> Many thanks for your help.
> 
> Best,
> Kyle
> 
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