[Chimera-users] Reflection symmetric

Tom Goddard goddard at sonic.net
Tue Nov 22 11:26:07 PST 2016

Hi Grzegorz,

  Chimera doesn’t support making the transformation from 3d grid indices to physical coordinates containing an inversion.  In theory it could since it just treats this transformation as a general affine transform (multiplying by an arbitrary 3x3 matrix, then shifting by a 3-vector).  But to make it easy for users to control this transform it converts it into a rotation axis and angle, scale factors, and skewing, and does not include the possibility of inversion.  So if you read a Chimera *.cmap file or some otther format (e.g. DX used by APBS maps), you will get an error from Chimera.  In principle the file formats that allow a 3x3 matrix can handle it, but Chimera cannot.  On the rare occassions when Chimera users have wanted to change the handedness of a 3d image the standard approach is to flip the z-stack of images with command "vop zflip #2” as Elaine mentioned.

  There are more problems with left-handed coordinate systems for maps in Chimera.  Contour surface normal vectors will point inward instead of outward messing up the lighting appearance.


> On Nov 22, 2016, at 4:18 AM, Grzegorz Bokota <g.bokota at cent.uw.edu.pl> wrote:
> Thanks for your response. I need some time to check it. I see thet it is realized by reversing volumetric data in z-dimesion and recalculating rotation axis and angel. it is impossible to be done by some parameters?
> Grzegorz Bokota
> 2016-11-09 19:33 GMT+01:00 Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>:
> Hi Grzegorz,
> I’m not sure if this is exactly what you mean, but when the data has been opened in Chimera you can use the “vop zflip” command to create a new data set with the Z planes in the opposite order:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zFlip <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zFlip>>
> 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 Nov 8, 2016, at 9:35 AM, Grzegorz Bokota <g.bokota at cent.uw.edu.pl <mailto:g.bokota at cent.uw.edu.pl>> wrote:
> > Hi,
> > I need to apply isometry and shift to volume data. In cmap file format it is possible to do rotation
> > but to have isometry I need to can do symmetric reflection. Ir is possible with any chimera format?
> > I found that there is "symmetries" parameter in cmap file format, but i do not seen any effect.
> >
> > Sincerely,
> > Grzegorz Bokota
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