[Chimera-users] When structures and density maps don't align

Walter R.P. Novak wnovak at brandeis.edu
Mon Sep 10 09:37:52 PDT 2007

Hi All,

Amongst my colleagues (to whom I constantly evangelize Chimera) there  
is often an issue opening pdb and map files together. Specifically,  
sometimes the maps and pdb coordinates are not superimposed (often  
drastically). I have been able to reproduce the issue so let me  
explain what works and what doesn't.

What works: If you take a pdb file and an mtz into Phaser (from the  
ccp4 suite) then refmac for rigid body refinement and convert the  
output mtz to a map using mapman it works. The pdb and map  
superimpose perfectly.

What doesn't work: If you take a pdb file (of known correct solution  
but not transformed to the correct coordinates) and throw it into  
refmac (ccp4) and do some rigid body refinement and then convert the  
resulting mtz into a ccp4 map, the map is perfectly good (the  
statistics are identical to using the phaser placed model), but when  
opened in Chimera they do not superimpose.

Both of the methods above appear valid as far as structure  
determination (R and Rfree are identical, etc) and I know coot will  
align the model and map and I believe pymol will too, though I don't  
use pymol personally so I cannot vouch for that.

Is the correct transformation information hidden in a file somewhere  
so that Chimera can align the two files automatically. Often people  
skip the phaser step and drop the model right into refinement and  
then manually aligning in Chimera becomes difficult.


Walter R.P. Novak, Ph.D.
Postdoctoral Fellow
Rosenstiel Basic Medical Research Center
Brandeis University
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405

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