[Chimera-users] Reflection symmetric

[Tom Goddard]

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.

	Tom



> 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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