It was a bad idea. What Jason initially suggested (save left-eye and right-eye) should work. What I have to manipulate images is only gimp, with which I am not very familiar. But it seems to have the capability of arranging the two saved files so as to get a stereo effect. There is even a (unofficial) plugin to remove unwanted space around. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret@gmail.com> Date: Tue, Feb 24, 2009 at 9:31 AM Subject: Re: [Chimera-users] stereo view To: Elaine Meng <meng@cgl.ucsf.edu> Hi Elaine: That makes problems as the referee just wants a stereo view of details of the binding site, which requires magnifying the figure. Is it any way to save a pdb file of the magnified zone alone? (to start from there to build a stereoview). Of course, the normal  pdb saving of a magnified figure saves the coordinates for the whole. The only way I can conceive to get the coordinates of the binding site, and nothing else, is manually deleting rows from the pdb file. A tricky route because the chains start and return to the starting point and the binding site is on both strands. thanks francesco On Tue, Feb 24, 2009 at 1:27 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

I guess you could also save separate left eye and right eye images and put them farther apart.  That might also mess up the stereo effect, though. Elaine

On Feb 23, 2009, at 4:26 PM, Elaine Meng wrote:

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Hi Francesco, There is a certain separation needed or else your eyes cannot form the stereo image.  You could try zooming out so the atoms don't take up the whole window, or adjusting parameters in the Camera tool (under Tools -> Viewing Controls) but I usually don't mess with those camera parameters because you could disrupt the stereo viewing if you change them very much. Elaine

On Feb 23, 2009, at 3:06 PM, Francesco Pietra wrote:

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Hi Elaine: Is it any direct way to save stereoimages from magnified images? By the normal route, the wall-eye couple of images are saved adjacent to one another, with no space in between them.

thanks francesco

On Tue, Feb 17, 2009 at 1:43 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

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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": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>

(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 right.

(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.

Best, Elaine ----- Elaine C. Meng, Ph.D.                          meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco                    http://www.cgl.ucsf.edu/home/meng/index.html

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

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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, 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.

-Jason

Quoting Francesco Pietra <chiendarret@gmail.com>:

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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"?