[Chimera-users] drawing parallelepiped
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
> 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
> both (a) and (b) require you to figure out coordinates for the corners
> (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
> 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 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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