[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
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
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.
Rosenstiel Basic Medical Research Center
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405
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