[Chimera-users] locating models in maps by unit cell transformations

Thomas Goddard goddard at cgl.ucsf.edu
Thu Feb 7 17:25:15 PST 2008

Hi Trevor,

   Chimera doesn't move a crystallography unit cell map around to cover 
the PDB model you are looking at, as does O and Coot.  Basically Chimera 
map capabilities were created primarily for electron microscopy maps 
that are not periodic.  Still I agree that is useful for many people and 
we should add that to Chimera and I'll put it on our requested feature list.


   There are harder ways currently in Chimera to get the PDB model and 
map to coincide in cases where they don't when they are first opened. 
One is to shift the map by hand.  Use the volume dialog Coordinates 
panel and add an integral number of unit cell shifts to the x, y, or z 
axes.  You'd have to look at the CRYST1 record in the PDB file to know 
the unit cell size, or show the Unit Cell dialog (menu Tools / 
Higher-Order Structure / Unit Cell).  If the cell angles are not 
90,90,90 then it is trickier to figure out the xyz translations.

   Coot and maybe O too also will "wrap" the periodic map if the PDB 
crosses the map unit cell box into the next unit cell.  In Chimera two 
copies of the map could be made (volume dialog menu file / duplicate), 
one translated by a unit cell size, and turning off "cap box faces" in 
the volume dialog surface and mesh options.  Actually I see this does 
not work since Chimera knows that the two maps are the same and applies 
the same translation to both.  That needs fixing.  Even if it worked it 
is a lot of trouble.  Again Chimera should do the wrapping.  Since most 
Chimera map users look at electron microscopy it will need to be an 
optional behavior when added to Chimera.  I will add this too the 
requested features page.


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