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@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
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. Tom 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@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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participants (2)
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Elaine Meng -
Tom Goddard