Hello Tom, Thanks for the answer... It is a nice alternative. Although, it's kind of more difficult to manually translate a precise amount of nm. Is there a way, like with the "plane" option, to control precisely the width and the translation of the subregion box? Maybe through a command line, but I have found it... Thanks again for the help, Nicolas *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* _____ From: Tom Goddard [mailto:goddard@sonic.net] To: Nicolas Coudray [mailto:ncoudray@nysbc.org] Cc: chimera-users@cgl.ucsf.edu Sent: Wed, 07 Dec 2011 19:00:01 -0500 Subject: Re: [Chimera-users] Axis vs map rotation Hi Nicolas, To show an oblique slice of a map you can use the volume dialog "subregion selection" panel. The "planes" panel can only display slices perpendicular to the volume axes as you found. There's a video showing how to show the oblique slice on the Chimera video tutorial web page http://www.cgl.ucsf.edu/chimera/videodoc/slice/index.html The Chimera volume guide has a text description of the procedure. http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#re... Tom Hi, I'm using the "Feature >> Plane" options of the "Volume viewer tool" to show contour lines in planes of density maps. For the plane, there are 3 options: "X-axis", "Y-axis", and "Z-axis". The plane I'm interested in is none of those. I try to rotate the maps, but the X, Y and Z axis are also rotating... Do you know if there's a way to rotate the "axis" and the "map" independently, please? Thanks in advance, Nicolas

Hi Tom, Thanks a lot for the answers. It is really helpful and it's exactly what I needed. I also realized that to precisely rotate the box, I can read the value of the rotation when I open the "Features>>Coordinates" option. Best, Nicolas *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* _____ From: Tom Goddard [mailto:goddard@sonic.net] To: Nicolas Coudray [mailto:ncoudray@nysbc.org] Cc: chimera-users@cgl.ucsf.edu Sent: Thu, 08 Dec 2011 19:17:49 -0500 Subject: Re: [Chimera-users] Axis vs map rotation Hi Nicolas, There is not a command to shift or position an oblique volume slice. I agree that would be useful and will put a feature request in our database for it. Here's a way to do what you want. Use the subregion selection green outline to crop to a rotated box. Make the box have a thickness that covers your structure of interest. This creates a new volume shown in the volume dialog and you can use the Planes panel to flip through planes of that rotated volume separated by precisely the grid spacing. The grid spacing can be specified using the entry field at the end of the "Rotate selection box" line in the subregion panel. It defaults to match the original data set grid spacing. To control the width and height of the rotated volume you can use the Region Bounds panel of the volume dialog to specify exactly how many voxels to use along each axis for display of the rotated volume. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Axis vs map rotation From: Nicolas Coudray To: Tom Goddard Date: 12/8/11 6:08 AM Hello Tom, Thanks for the answer... It is a nice alternative. Although, it's kind of more difficult to manually translate a precise amount of nm. Is there a way, like with the "plane" option, to control precisely the width and the translation of the subregion box? Maybe through a command line, but I have found it... Thanks again for the help, Nicolas *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* _____ From: Tom Goddard To: Nicolas Coudray Cc: chimera-users@cgl.ucsf.edu Sent: Wed, 07 Dec 2011 19:00:01 -0500 Subject: Re: [Chimera-users] Axis vs map rotation Hi Nicolas, To show an oblique slice of a map you can use the volume dialog "subregion selection" panel. The "planes" panel can only display slices perpendicular to the volume axes as you found. There's a video showing how to show the oblique slice on the Chimera video tutorial web page http://www.cgl.ucsf.edu/chimera/videodoc/slice/index.html The Chimera volume guide has a text description of the procedure. http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#re... Tom Hi, I'm using the "Feature >> Plane" options of the "Volume viewer tool" to show contour lines in planes of density maps. For the plane, there are 3 options: "X-axis", "Y-axis", and "Z-axis". The plane I'm interested in is none of those. I try to rotate the maps, but the X, Y and Z axis are also rotating... Do you know if there's a way to rotate the "axis" and the "map" independently, please? Thanks in advance, Nicolas