I am experiencing a strange phenomenon when I open maps in Pymol.
I have a Chimera session with a PDB file docked into a CCP4 map. If I
display the unit cell in Chimera the density is centered in the unit
cell.
If I open the exact same map and PDB file in Pymol, the model and map
are no longer in agreement, and when I display the unit cell in Pymol
the map is situated at the corner of the unit cell rather than in the
center.
I have found that if I translate the PDB model by _roughly_ half the
unit cell length (in all dimensions) I arrive at where it is normally
situated in Chimera. But even this is not exact, and it appears to be
half the unit cell dimensions + ~10A.
I am just trying to understand how this map is being interpreted by
Pymol and what known ambiguities or assumptions are made when it is
loaded that might cause this behavior.
Thanks
Albion
Here is the maps info from MAPMAN
Grid = 96 96 96
Origin = -48 -48 -48
Extent = 96 96 96
Cell = 213.423 213.423 213.423 90.000 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
