[Chimera-users] Can Chimera measure the molecular size?

[Elaine Meng]

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/structuremeas.html#distances 
 >
<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/ensembletile.html 
 >
<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/measurevol.html 
 >

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
>