[Chimera-users] stereo view

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 16 16:43:47 PST 2009

Hi Francesco,
All of Jason's suggestions are good (thanks Jason!), and I only wanted  
to add a few things:

(1) while the window will always be a rectangle, you could resize it  
so that there is a different ratio between height and width.  If your  
long molecule is oriented across, you could resize the window to be  
less tall so that the width:height ratio is greater.  Don't worry if  
the window is then filling less of your screen -- you can specify as  
high a resolution as you want in the File... Save Image dialog.  Of  
course, with a given window size, you should scale up your molecule(s)  
to fill it as much as possible.   In agreement with Jason, I think  
usually a white background is better than black for publication  
purposes.  How to change background color is described near the top of  
the "Tips on Preparing Images":

(2) There is a section on saving stereo images near the bottom of that  
"Tips on Preparing Images" page (by the way, you can use "Help...  
Search Documentation" to look for help topics such as "stereo  
image").  I think journals usually show the "wall-eye" type of stereo,  
which can be achieved by saving one image in the wall-eye stereo mode,  
or by saving separate left and right views and placing them side by  
side with the left-eye view on the left and the right-eye view on the  

(3) just show the surface, adjust clipping and depth-cueing as Jason  
suggested, and use your artistic and scientific judgement as to  
whether it improves your image!  There are additional suggestions for  
improving surface appearance in the "Tips on Preparing Images" page.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 16, 2009, at 2:04 PM, odonnell at chem.fsu.edu wrote:

> 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.
> -Jason
> 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"?

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