[Chimera-users] Chimera_v1.2470

[Tom Goddard]

Hi Brittney,

  The solid box you see when opening some maps I suspect is caused by 
the new option to "cap high values at box faces" that is in the volume 
dialog Surface and Mesh options panel.  This means that if the 
contouring level is lower than the volume data values at a face of the 
volume box then the box face appears solid.  You can turn this option 
off then make that the default using volume dialog menu entry Features / 
Save Default Dialog Settings.

  This is particularly a problem if your map is inverted -- that is, 
high density corresponds to negative data values.  I guess when you say 
you solve the problem by converting from PIF format to MRC you also 
invert the map values (v -> -v).  The file format has no effect on how 
the data appears, only the data values matter.

    Tom