[Chimera-users] Axis vs map rotation

[Nicolas Coudray]

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

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From: Tom Goddard [mailto:goddard at sonic.net]
To: Nicolas Coudray [mailto:ncoudray at nysbc.org]
Cc: chimera-users at 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
        
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From: Tom Goddard
          To: Nicolas Coudray
          Cc: chimera-users at 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#resample
          
            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
            
                    
                
            
          
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