[Chimera-users] distance measurements on surfaces

Thomas Goddard goddard at cgl.ucsf.edu
Thu Jul 10 17:21:49 PDT 2008

Hi Daniel,

   You can place markers on a single plane of volume data by turning on 
the "Place markers on data planes" option in the volume tracer dialog 
Mouse menu.  This option is in current Chimera versions and the older 
1.2509 you are using, but not in the Nov 2007 production release 
(1.2470).  This should allow you to measure distances on the plane.

   I played with AFM data of virus crystals using Chimera a few years 
back.  Might interest you.



Daniel Hautzinger wrote:
> Dear all,
> from the Volume Visualization Tour, I discovered the topography  
> command that now allows me to dsiplay atomic force microscopy data  
> (basically bitmap images with grey scales representing height). In  
> that way I got some very nice images. I also found out how to scale  
> the voxel size, so the scale of the structures should be correct. To  
> test this, and to be able to add some length markers, I wanted to  
> measure distances on the surface generated by the topography command.  
> But while that seems possible for volume data (by setting markers), I  
> had no success with the surface representation of my data nor the  
> original image (which is handled as kind of a volume, but a single  
> slice) when it came to setting markers or measuring distances in  
> another way. Did I miss anything, or is that just not possible? I am  
> using build number 2509, because of the topography feature. Setting  
> markers is described as working by setting the marker in the first  
> maximum in the line of sight at the click position. For surfaces, you  
> could just take the position of the visible pixel clicked. Or maybe it  
> is possible to convert surfaces to volumes?
> Thank you for your help
> Daniel Hautzinger
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