Re: [Chimera-users] Save session for movie
Hi Francesco, On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote:
If at all, I did not understand if a continuous trace of the centroid (instead of a series of balls) can be obtained in the context of the protein. That would improve the presentation further. Otherwise, the series of balls for the centroid, with appropriate choice of radius and step size, shows the pathway of the ligand through the protein adequately.
Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (BILD format) showing lines/cylinders connecting the centroid centers.
As a minor point, I was unable to render helices transparent. Transparency would help to to see the centroid trajectory in between helices.
Should be possible unless there's something wrong with your graphics cards. Try this: Select->Structure->secondary structure->helix Actions->Color->from editor This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that: (note the "Opacity" box is checked) and the structure looks like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
As a minor point, I was unable to render helices transparent. Transparency would help to to see the centroid trajectory in between helices.
Eric described one way to make transparent ribbons. The "similar binding sites" tutorial gives examples of how to do it with commands: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html
and both ways were described in more detail in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001155.html
Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Does Chimera has a function to measure the size of a molecular? If I have several protein, how to display the structures side by side, with the size of the images corresponding to the actual size of the molecules. Thanks, Jianbo
Hi Jianbo, You can measure the distance from one atom to another, but you'd have to decide which two atoms to use: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> Then you could their VDW radii if you wanted, as the distance is measured between the atom centers, not their surfaces: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> There are some other ideas, such as measuring principal axes, in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005083.html> These methods measure the structures directly, which is better than trying to compare the sizes of the images of the structures. However, if you need to make an image where the relative sizes are correct, (a) the structures should be in a plane parallel to the screen, and (b) turn off "perspective" and instead use the orthographic projection. To get the structures in a plane parallel to the screen, you could first superimpose them so that they are all basically in the same place, then "tile" them (spread them out in a plane). How you would superimpose them depends on whether the structures are similar to each other or not. This page summarizes ways to superimpose structures: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Tiling could be done with Tile Structures (under Tools... Structure Comparison) or the "tile" command: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensembletile/ensemb...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/tile.html> Changing from perspective to orthographic projection can be done in Camera (under Tools... Viewing Controls) <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sideview.html#camera> or the command "set projection orthographic": <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> Yet another issue is whether you wanted to just measure length, or if you are interested in volume. You could measure the volume enclosed in a molecular surface with the Measure Volume and Area tool (under Tools... Volume Data): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurev...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 18, 2010, at 2:56 PM, Dong, Jianbo wrote:
Does Chimera has a function to measure the size of a molecular? If I have several protein, how to display the structures side by side, with the size of the images corresponding to the actual size of the molecules.
Thanks, Jianbo
participants (3)
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Dong, Jianbo -
Elaine Meng -
Eric Pettersen