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