[Chimera-users] Multi-scale models and BIOMT

Tom Goddard goddard at cgl.ucsf.edu
Fri Dec 14 14:30:00 PST 2007

Hi Ken,

  Here's what's going on.  You have BIOMT matrices in your PDB file that 
specify the rotations and translations that operate in the coordinate 
system of the EM map.  This is just what the Chimera "sym" command 
expects.  The multiscale model tool though assumes that the BIOMT 
matrices act in the coordinate system of the PDB atoms.  It knows 
nothing about the volume.  The trouble is that you've moved the PDB 
model relative to the map using "Fit model in map".  So the coordinate 
frame for the PDB atoms is no longer aligned with the coordinate frame 
of the EM map.  In some cases this is what you want.  For example if 
your BIOMT matrices said how to make an icosahedral virus from a 
monomeric subunit, you'd want it still to make the correct icosahedron 
if you first fit the monomer into a density map.  But in your case it 
isn't so nice since your BIOMT matrices are defined relative to the map 

  Here's the fix.  Fit your PDB model into the map, then use File / Save 
PDB..., turn on the "Save relative to mymap.mrc" option and save the new 
PDB.  Put the BIOMT matrices in that PDB file that has already been fit 
into the map and multiscale will work with it.


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