[Chimera-users] Displaying volumes with negative densities

Tom Goddard goddard at cgl.ucsf.edu
Mon Mar 24 09:06:48 PDT 2008

Hi Julio,

  If you are creating volume contour surfaces where the objects of 
interest have more negative data values then you should turn off the 
"cap high values at box faces" option in the volume dialog surface and 
mesh options panel.  Since you view these inverted density maps often 
you probably want to save that setting using volume dialog menu entry 
"Features / Save default dialog settings" so Chimera will use it in 
future sessions.


Dr .Julio Ortiz wrote:
> Dear Thomas,
> I noticed that when displaying volumes as isosurfaces we can not 
> visualize negative densities. The volumes turns a solid cube bellow 
> cero. I can imagine that  with volumes coming from some programs of 
> SPA like in EMAN, this is not a matter, because they use 
> protein=white. But we are always using protein=black.
> I wanted to ask you if there is a simple way to correct that, because 
> I love to use chimera for fast check of my volumes and it will be not 
> fun to change the contrast each time.
> Just for your info: the last version that works for me was: 
> chimera-1.2422-win32
> Greetings,
> Julio

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