[Chimera-users] stereo view
odonnell at chem.fsu.edu
odonnell at chem.fsu.edu
Mon Feb 16 14:04:54 PST 2009
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,
try DEPTH CUEING under TOOLS=>VIEWING CONTROLS=> EFFECTS. tweak the
"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>:
> 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
> 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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