[Chimera-users] a question relate to Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 27 09:50:26 PDT 2015


On Aug 26, 2015, at 6:27 PM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear Elaine,
> Thanks for the reply.
> 
> Here let us consider the first question on "a particle has a diameter of 100 pixels ", which I think may be done by Chimera with your help. From http://www.imagescience.de/fsc/index.htm, we can download a software which can be used to calculate the resolution of the map by FSC. When we use that software for calculation, we need to input "Filling degree" D/L, where the value of object size D in voxels, and the L, the linear ssize of the 3D volume (x, y,z). A typical value of "Filling degree" D/L would be 0.66, indicating that 2/3 of the linear width of the 3D volume is filled by the object.
> 
> Thus will you please show me by Chimera how can we know "the value of object size D in voxels"?
> 
> I am looking forward to getting your reply.
> 
> Best regards.
> Smith

Dear Smith,
Please send Chimera questions to chimera-users at cgl.ucsf.edu (instead of to me directly).   Others may be able to answer your questions better than I can, for example in this case where I don’t know the answer. 

For linear size of the whole volume (the map), we already discussed that you can see the number of grid units (voxels) in X,Y,Z to the right of the dataset name in the Volume Viewer dialog, and see angstroms per grid unit in the Features: Coordinates section of Volume Viewer.  You could multiply the values to get the size of the map in angstroms.
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011437.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011433.html>

However, I don’t know how you could measure the voxel size of the object in Chimera.  As far as I know you could only estimate it by eye, or by measuring angstrom dimensions, converting to grid units, and then multiplying them to roughly estimate the area of the object in voxels.  It would only be an estimate, assuming your object is not a perfect circle or square.  See previous posts on measuring angstrom dimensions in a map:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010609.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009503.html>

My guess is that people would normally get this information from the software used in the original data collection, not by doing measurements in Chimera.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco





More information about the Chimera-users mailing list