[Chimera-users] Fwd: stereo view

Francesco Pietra chiendarret at gmail.com
Tue Feb 24 08:26:42 PST 2009

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.


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Tue, Feb 24, 2009 at 9:31 AM
Subject: Re: [Chimera-users] stereo view
To: Elaine Meng <meng at 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.


On Tue, Feb 24, 2009 at 1:27 AM, Elaine Meng <meng at 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:
>> 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:
>>> 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 at cgl.ucsf.edu> wrote:
>>>> 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 at 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 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"?

More information about the Chimera-users mailing list