Inspecting electron density maps

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Download coordinates and structure factor file

  1. Download 3ODU.pdb
  2. Download 3odu-sf.cif [1]

Open coot

/raid3/software/coot/coot-0.6-Linux-x86_64/bin/coot &

Load molecule and map

  1. File-> Open Coordinates -> 3ODU.pdb
  2. File-> Open MTZ, mmCIF, fcf or phs.. -> 3odu-sf.cif
  3. Draw -> Go to atom > Chain A, residue 1500 -> Apply

Coot ABC

  • A) Rotate with left mouse button
  • B) You can center the view by clicking on the atom of interest with the middle mouse button
  • C) Zoom with right mouse button

Pymol instructions: Here are the pymol lines to load the maps (for A2A in this case, sigmalevel 1 using second line). The map here is in ccp4 format, but other will work too (but depends on your pymol version):

load 3eml.ccp4,map1
isomesh msh1,map1,1
load 3eml.pdb