[Chimera-users] drawing parallelepiped

Tom Goddard goddard at cgl.ucsf.edu
Mon Feb 23 10:00:58 PST 2009

There is a hidden capability to draw a bounding box for each model but 
there is no user interface for it.  To use it start the Python shell 
Tools / General Controls / IDLE and type

    chimera.viewer.showBound = True

It shows a separate box for each model and does not let you show boxes 
for some models and not others.


Elaine Meng wrote:
> On Feb 23, 2009, at 3:31 AM, Francesco Pietra wrote:
>> For mono view figures, I wonder whether Chimera allows enclosing the
>> model in a parallelepiped. This would confer a sense of depth to a
>> very complex model (a complex of two proteins, partly in a lipidic
>> membrane.
> Hi Francesco,
> There are a few different possibilities:
> (a) make a PDB file with "atoms" at the corners and the desired bonds  
> (described in CONECT lines), show as wire or stick.
> The Crystal Contacts tool uses that trick, but is unlikely to generate  
> what you want in this case.  You could try creating it interactively  
> with markers and links using Volume Tracer, but probably just creating  
> a PDB file in a text editor would be easier.
> (b) make a file in BILD format describing the parallelpiped outlines  
> -- requires similar information as the above:  coordinates of points  
> at the corners and which points should be connected
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
> both (a) and (b) require you to figure out coordinates for the corners  
> yourself...
> (c) a devious but easy way if you don't mind a rectangular box (all  
> angles 90 degrees) is to use the "molmap" command to create a density  
> map from the displayed atoms, but hide that map's contour surface and  
> just show the box around it.  For example, use the command:
> molmap @/display 2
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
> Then in the Volume Viewer dialog that appears, choose "Features...  
> Data display options" and turn on "Show outline box" and also choose  
> "File... Remove Surface."  In that dialog you can also specify the  
> color and linewidth of the outline.
> For conveying depth, you can also try adjusting the clipping planes in  
> the Side View.  If you put the back one closer to the atoms, the depth  
> cueing "fog" will be more obvious.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
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