[Chimera-users] images from ChimeraX

Thu Nov 7 14:57:16 PST 2019

Hi Mike,

  One last thought (I hope it is the last!).  ChimeraX has a camera mode called side by side, enabled with command "camera sbs".  This shows left and right eye images and is for recording videos that use SBS format.  It behaves just like wall eye stereo.  There is a parameter that controls the depth of field (which adjust the angle of rotation between the left/right views), "camera sbs eyeSeparation 10".  Here the number 10 is in Angstroms, the separation of the left and right cameras in the scene.  You can preview this cross-eye but the depth will be inverted because the left and right eye images need swapping from cross eye.  If it worked you could swap left and right panels by just cutting each out in a photo editing program.  Alternatively you could use negative eye separation, then it seems to work as cross-eye but the image separation is bit weird.

  There were errors when I used ChimeraX camera sbs and resized the window.  I fixed those today.  The errors are harmless -- just warning that OpenGL resources were not deleted.  But tonight's ChimeraX won't have those errors.

	Tom

> On Nov 7, 2019, at 1:59 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Mike,
> 
>   I just noticed the subject of your message said ChimeraX.  All my answer was about Chimera, not ChimeraX.  (There is a separate ChimeraX mailing list chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>).
> 
>   Here are ChimeraX tips.  So in ChimeraX there is no cross-eye stereo mode (yet).  So I would suggest using the two side-by-side ChimeraX windows.  There is an icon in the lower right corner that hides all the tool panels at the right edge so the graphics is the full window width.  Use the windowsize command to get the right aspect ratio (e.g. windowsize 900 1200).  Use a saved session.  Rotate one image with "turn y 6".  Use the File / Save... dialog and choose PNG image and set pixel size to be 300 times desired print width in inches.  One thing that could be a bit weird is if you use full lighting then it casts a direct shadow and the left and right eye direct shadows won't match since the light direction is fixed to the view direction (ie the light does not rotate 6 degrees, so the left and right eye won't see the same lighting).  Soft lighting only has isotropic shadows so won't have that problem.  If the direct shadow is a problem you could rotate the light using the "lighting" command.  Use lighting with no options to show the current direction vector for the light, then calculate a rotated direction 6 degrees and set it with the "lighting direction x,y,z" command.
> 
> 	Tom
> 
> 
>> On Nov 7, 2019, at 1:47 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> You might also set "supersample 1x1".  The default 3x3 setting makes the image 3 times bigger on each axis and then bins down by a factor of 3.  Making it 3 times larger make cause the graphics to fail on such a large image.  And at 300 dots per inch the 3x3 supersample won't have a visible effect.
>> 
>> 	Tom
>> 
>> 
>>> On Nov 7, 2019, at 1:45 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>>> 
>>> Hi Mike,
>>> 
>>>   The panel shown by File / Save Image... says pixels "Units pixels".  
>>> 
>>> 	Tom
>>> 
>>> <Screen Shot 2019-11-07 at 1.44.52 PM.png>
>>>> On Nov 7, 2019, at 1:34 PM, Schmid, Michael F. <m-schmid at slac.stanford.edu <mailto:m-schmid at slac.stanford.edu>> wrote:
>>>> 
>>>> Hi-
>>>> Thanks. That really helps! So the “width” and “height”, if just given as 5400 and 7200, respectively, will be understood as pixels, or do you have to say “5400 pixels”?
>>>>  
>>>> From: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
>>>> Date: Thursday, November 7, 2019 at 1:28 PM
>>>> To: "Schmid, Michael F." <m-schmid at slac.stanford.edu <mailto:m-schmid at slac.stanford.edu>>
>>>> Cc: "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
>>>> Subject: Re: [Chimera-users] images from ChimeraX
>>>>  
>>>> 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.
>>>>  
>>>> Tom
>>>>  
>>>>  
>>>>  
>>>> 
>>>> 
>>>> On Nov 7, 2019, at 9:48 AM, Schmid, Michael F. <m-schmid at slac.stanford.edu <mailto: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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>> 
> 
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