[Chimera-users] images from ChimeraX

Tom Goddard goddard at sonic.net
Thu Nov 7 13:27:56 PST 2019

Hi Mike,

  To avoid pixelation make sure to save the left and right eye images at high resolution.  Using Chimera File / Save Image... you would set the image size in pixels to be maybe 300 times the number of inches wide you will make the image (so if one eye image is 18 inches wide that use image width 5400 pixels).

  For surface rendering of the tomogram make sure step is 1 in volume viewer so it is using the full resolution data.

  For getting the right angle of rotation between the two images I would suggest that you display it on a large flat panel screen (e.g. 50" TV)  if you have one at the size you want to print at and check visually how well the cross-eye stereo pair is working.  Make the Chimera window aspect ratio exactly match what  you will print (e.g. 36 x 24n inches would be 3 to 2), for example use Chimera command "windowsize 1800 1200".  In Chimera you can use the "cross-eye stereo" camera in the side view (menu Favorites / Side View) Camera tab in the "camera mode" menu.  Then you can fiddle a bit with the focal plane by going to the Side View tab, choose "Side: top" and drag the vertical dashed yellow line left or right.  It represents the focal plane.  I'm not sure what that means for cross-eyed stereo but it effects the angle of rotation between left and right images.  I tried this on my 24 inch wide screen (so not as big as you will print) and I really have to stand far back (5 or 6 feet) to comfortably look at it, otherwise the floating image is too close to my face and I think my eyes don't like to converge that close while still focusing 5 feet away.  If this cross-eye stereo mode works for you, you can use File / Save Image... and it will save the two eyes as a single image.

  If that cross-eye stereo mode isn't working well for you you could open two copies of Chimera side by side and rotate the image of one relative to the other with the command "turn y 6" to rotate one view by 6 degrees.  You might first save a session in the desired orientation that you open in both Chimera copies then rotate just one of them.

  I think the key here is to try it on a screen to see if it is giving you what you want before you print.


> On Nov 7, 2019, at 9:48 AM, Schmid, Michael F. <m-schmid at slac.stanford.edu> wrote:
> Hi-
> I am trying to make a high resolution image of a surface rendering of a tomogram. The final size of the image(s) will be 18 in x 24 in. It is for a wall display. How do I do it for the best (minimally pixelated) result? I presume I will have to adjust the triangle rendering of the maps to be included, and also the rendering of the final images (for a stereo pair). Also, I assume I have to render them at ~6 degrees total tilt with respect to each other.
> Thanks,
> Mike
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