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6. Viewing G-factors in 3D

A simple utility program called gfac2pdb is provided with PROCHECK to allow you to visualize a given structure's dihedral angle G-factors in 3D using any standard molecular graphics software package.

The program generates an output file in PDB format with the following atoms' temperature factors replaced by values representing the G-factors of the corresponding torsion angles:-

    G-factor              Atoms
    --------              -----
    phi-psi               N and CA
    omega                 Backbone C
    chi1-chi2             CB and CG
    chi3                  CD
    chi4                  CE

All other atoms' temperature factors are set to 0.

You can view the output PDB file using any molecular graphics program (such as QUANTA or RasMol), and colour the atoms according to B-value. The red regions of the structure will be those with unusual torsion angles, corresponding to negative G-factors.

Any large regions of redness might indicate parts of the structure that need further attention. However, please note that some programs (eg RasMol) scale the colours according to the maximum and minimum B-values they encounter in the file. So, there will always be red regions, corresponding to the maximum B-values, irrespective of how large or small the absolute values of those B-values are.

You can overcome this problem by, say, inserting a dummy atom into your displayed PDB file which has a B-value of 80.00 (which is the maximum value that gfac2pdb gives). The atom might, for example, be:

HETATM    1  N   XXX     1       0.000   0.000   0.000  1.00 80.00

In RasMol you can "hide" this atom by using the command "select not xxx".


 All atoms  Mainchain atoms

Running gfac2pdb

Before running gfac2pdb you must first run PROCHECK on your structure so that all the G-factors are calculated.

Then, to run gfac2pdb, enter:

    gfac2pdb coordinate_file


  • coordinate_file is the name of the PDB coordinates file.

For example,

    gfac2pdb 1abc.pdb

The output file will be called 1abc_gfact.pdb.

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