Mirrored density artefact
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
Hi Kyle, Apologies, it may be a while before this question can be addressed since our expert in this area (and who implemented vop) is away now and for the next couple of weeks. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 24, 2016, at 3:51 PM, Morris, Kyle Kyle.Morris@warwick.ac.uk 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
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
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom,
Works perfectly on my EM map, thanks for direction to this and the info.
Best wishes, Kyle
On 8 Apr 2016, at 03:56, Tom Goddard goddard@sonic.net wrote:
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
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Morris, Kyle -
Tom Goddard