[Chimera-users] Map Oddities

Albion Baucom baucom at msg.ucsf.edu
Fri Sep 22 10:41:24 PDT 2006

	I am trying to work out how maps are handled in various graphics  
programs so I can easily move between programs and expect to see the  
same thing in each session. Unfortunately at the moment that isn't  
working so well, and I would like to resolve this issue.

Basically I have a situation where I have a PDB model and a CCP4  
format EM density map in Chimera that are docked. When I open the  
exact same map and model in other programs such as O or Pymol, the  
map and the model are no longer in agreement.

What I have noticed is that if I draw the unit cell for the map (P1  
symmetry since this is an EM reconstruction), in Chimera, the model  
and map live in the center of the unit cell and are docked. If I draw  
the unit cell for O or Pymol, the map lives at the origin of the unit  
cell, at (0,0,0), which is in the corner, and model is outside of the  
unit cell offset by what appears to be some arbitrary translation (I  
have tried using half the unit cell dimensions as a translation, but  
that unfortunately gets me _very_ close to being correctly docked in  
the map, but off by some 10A).

It appears Chimera is handling the map and model differently than the  
other packages and I am trying to get an idea of what happens when  
this map is loaded. I am including a listing of the map header from  
MAPMAN below.



Grid        =         96        96        96
Origin      =        -48       -48       -48
Extent      =         96        96        96
Cell        =    213.423   213.423   213.423    90.000    90.000     
UVW         =          1         2         3
Spcgrp      =          1      Nr of points =     884736
Density min = -6.915E-01      Max          =  2.397E+00
Average     =  7.247E-11      Sigma        =  2.290E-01
Variance    =  5.243E-02
Mappage Prod=  8.257E+01      Plus         =         57
Dyn. range  = -6.903E-01      To           =  2.398E+00
Cell vol.   =  9.721E+06      Voxel vol.   =  1.099E+01
Grid vol.   =  9.721E+06      %Cell vol.   =     100.00
Origin frac =   -0.50000  -0.50000  -0.50000
Origin Cart =   -106.712  -106.712  -106.712
Top frac    =    0.48958   0.48958   0.48958
Top Cart    =    104.488   104.488   104.488
Spacing     =      2.223     2.223     2.223
Top         =         47        47        47
Changes     = F

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