[Chimera-users] stereo view

odonnell at chem.fsu.edu odonnell at chem.fsu.edu
Mon Feb 16 14:04:54 PST 2009

Hi Francesco,

   A couple of cents before the professionals respond with (very  
likely) better ideas:

In response to 1) Black is best for contrast but uses a lot of ink and money.
White should be fine.

n response to 2) If you go to TOOLS=>VIEWING CONTROLS=>CAMERA, you can  
select various camera modes. CROSS-EYE stereo will put your chimera  
graphic into cross-eye stereo. You can save an image as it is  
displayed on the screen. But i find saving two images, stereo left eye  
and stereo right eye better. Place these side by side in another  
graphic program, (e.g Adobe illustrator) and voila, stereo viewing.  
With two single images you can switch them around to alternate between  
wall-eye and cross-eye. Also, with two images its easier to make the  
distance between them a certain length, as journals are usually  
stringent about how the stereo images are displayed.

In response to 3)I'd to go TOOLS=>VIEWING CONTROLS=> SIDE VIEW and  
slide the back and front yellow planes. This will create a slab  
through your object removing other structural elements which might  
complicate the image. Also,
"start ratio and yon intensity to further remove emphasis on unwanted  
objects.  The Depth effects can make some really neat graphics

Hope this helps.


Quoting Francesco Pietra <chiendarret at gmail.com>:

> Hi:
> I would greatly appreciate advice about the following requests
> (between "".."") by the referees (interaction between two proteins;
> graphics by chimera):
> 1) "there is way too much wasted black space in figures".
> As the complex of proteins is elongated along one axis, I found it
> unavoidable to have wasted space around. Perhaps using a white
> background in the hope that white is less offending than black? Or is
> it a way to tailor the background according to the shape of the
> object?
> 2) "a stereoview might be helpful for better understanding".
> How to fulfill this request with chimera I have no idea.
> 3) "a molecular surface representation of the docking site would be useful".
> I read on passing about molecular surfaces on this forum. Is that
> feasible for the highly complex situation of 3D perspective with so
> many atoms at different "layers"?
> Thanks indeed for answering
> francesco pietra
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