[Chimera-users] Chimera VTK file reader

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 29 08:47:12 PDT 2013


Hi Andrew,
An easy way to change all the -32768 values to something like zero (so that the histogram in the Volume Viewer dialog will become useful) is with the "vop threshold" command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#threshold>

For example, if your VTK file is opened as model 0, you could create a new map model 1 in which all values below zero are set to zero with the following command:

vop threshold #0 min 0 set 0 model 1

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 Aug 27, 2013, at 3:20 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Andrew,
> 
>  I added a VTK file reader -- in tonight's Chimera daily build.  It handles vtk structured points files in ascii format like the one you gave me.  Your file had many -32768 values which seem to indicate regions where you don't have data and normal data values in a range 0 to 55.  This makes the histogram display of data values in Chimera worthless because the data range is 33000 but the meaningful range is 55.  Chimera is only able to show the whole range.  You might want to use some other value to indicate "no data", like -1 if negative values are not valid.
> 
> 	Tom
> 




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