[Chimera-users] volume visualization

Thomas Goddard goddard at cgl.ucsf.edu
Thu Jan 24 15:20:35 PST 2008

Hi Enrico,

   Sounds like you are doing everything right.  There was a CCP4 
alignment problem on some maps (when ncstart, nrstart, nsstart header 
parameters are far outside map bounds) in Chimera version 1.2444 and 
earlier.  Are you using a newer Chimera version?

   Another issue is if you have opened several files in Chimera and 
moved some relative to others, then open the map, the map will be 
aligned with the model having the lowest opened model id number which 
may not be the correct model to align with.  The Model Panel dialog 
Transform As... button allows you to correct this.

   You can look at the volume dialog "Coordinates" panel and see where 
the origin is set.  This is the physical x,y,z coordinates of grid index 
0,0,0.  If the value is 0,0,0 that indicates that the map header origin 
values were ignored because they were so large that they looked invalid. 
   (Unfortunately some maps do not initialize them.) You can change it 
if you can figure out the correct values though that should not be 

   You can send me the map and PDB if you want me to figure out the 
exact problem.


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