[Chimera-users] Saving Image of row stereo

Divita Mathur dmathur4 at gmu.edu
Tue Nov 17 14:49:21 PST 2020

I think that is what I will do. In fact, the screenshot I shared already has three copies of each of the green dyes. Thanks for looking into this!


From: Tom Goddard <goddard at sonic.net>
Date: Tuesday, November 17, 2020 at 1:34 PM
To: Divita Mathur <dmathur4 at gmu.edu>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Saving Image of row stereo

Hi Divita,

  I see.  If you want to depict that a molecule can be in various positions a better approach is to actually open 2 to 4 copies of it positioned slightly differently, maybe showing the copies as transparent.  Another approach is to save 5 copies of the image where you move the variable molecule a bit for each, then blend the images in Photoshop or Gimp.


On Nov 17, 2020, at 10:14 AM, Divita Mathur <dmathur4 at gmu.edu<mailto:dmathur4 at gmu.edu>> wrote:

Thanks for your response, Tom. I guess I should tell you what I am trying to achieve.

The row stereo image is interesting to me as it can be interpreted as a “vibrating” or “shaky” molecule (check attached). I want to represent that the green dye (and perhaps the underlying pink scaffold) is shaking and it is not constrained enough. Is there a camera setting that you can recommend?

The screenshot has these horizontal lines which I suspect have something to do with the quality of my computer screen.


Divita Mathur, PhD
Research Assistant Professor
George Mason University &
Center for Bio/Molecular Science and Engineering
Naval Research Laboratory
(202) 767-0687 (Office)
From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Date: Tuesday, November 17, 2020 at 12:58 PM
To: Divita Mathur <dmathur4 at gmu.edu<mailto:dmathur4 at gmu.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] Saving Image of row stereo

Hi Divita,

  I don't think Chimera can save the row interleaved image.  Such an image is not very useful since it would have to be positioned on a row interleaved stereo display (e.g. Zalman) with no scaling to appear 3d since even rows give one eye image and odd rows the other eye image.  Your best bet would be to try a screen capture program.


On Nov 16, 2020, at 6:23 PM, Divita Mathur <dmathur4 at gmu.edu<mailto:dmathur4 at gmu.edu>> wrote:

Hi all,

I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image?

Divita Mathur
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<Screen Shot 2020-11-16 at 9.30.16 PM.png>

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