Depicting BFactor

A program that depicts the B-factor of a ligand and its environment.

See also

• Visualizing Protein-Ligand B-Factor OpenEye Python Cookbook example

• Visualizing Protein-Ligand B-Factor Map OpenEye Python Cookbook example

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> java BFactor2Img --help

will generate the following output:

[-complex] <input> [-out] <output pdf>

Simple parameter list
    -height : Height of output image
    -width : Width of output image

    SplitMolComplex options :
      -ligandname : Ligand name

    input/output options
      -complex : Input filename of the protein complex
      -out : Output filename

    molecule display options
      -aromstyle : Aromatic ring display style

Code

Download code

BFactor2Img.java and BFactor2Img.txt interface file

See also

• OESplitMolComplex function in OEChem TK

• OENearestNbrs class in OEChem TK

• OEPrepareDepictionFrom3D function

• OESurfaceArcFxnBase class and OEDraw2DSurface function

• OEAtomGlyphBase class and OEAddGlyph function

Examples

prompt> java BFactor2Img -complex 1MEH.pdb -ligandname MOA -out MOA.png

will generate the following output:

Average BFactor of the complex = +32.721
Minimum BFactor of the ligand and its environment = +21.500
Maximum BFactor of the ligand and its environment = +72.060

and the image shown in Figure: Example of depicting the BFactor of MOA and its environment.

Example of depicting the BFactor of MOA and its environment

prompt> java BFactor2Img -complex 1LEE.pdb -ligandname R36 -out R36.png

will generate the following output:

Average BFactor of the complex = +23.754
Minimum BFactor of the ligand and its environment = +6.040
Maximum BFactor of the ligand and its environment = +32.050

and the image shown in Figure: Example of depicting the BFactor of R36 and its environment.

Example of depicting the BFactor of R36 and its environment