[Chimera-users] drawing parallelepiped

[Elaine Meng]

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