Coloring Methyls in Pymol

:: pymol

This post expands on yesterday’s post that was focused on coloring protein structures by residue in Pymol.

  1. Your data should be in a tab-delimited text file, formatted like this:

    2	ALA	CB	0.03416350
8	ILE	CD1	0.43143940
13	LEU	CD1	0.50597498
  2. Make sure you have downloaded data2bfactor.py from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/.
  3. Open pymol & load your protein structure.

  4. Run any scripts you want to use:

    PyMOL> run ~/scripts/data2bfactor.py
PyMOL> run ~/scripts/spectrumany.py

  5. You may want to set all the b-factor data for your protein to –1 or to some other number beforehand, because any residues not mentioned in your data file will retain their original crystallographic B-factor:

    PyMOL> alter MyProtein, b=-1

  6. Define a selection of all your methyls:

    PyMOL> select MyMethyls, (resn ALA and name CB)+(resn ILE and name CD1)+(resn LEU and name CD1+CD2)+(resn MET+MSE and name CE)+(resn VAL and name CG1+CG2)+(resn THR and name CG2)

  7. Display things nicely:

    PyMOL> hide lines
PyMOL> show cartoon
PyMOL> dss
PyMOL> color gray80, MyProtein
PyMOL> show spheres, MyMethyls
PyMOL> show sticks, resn ALA+ILE+LEU+VAL+MET and not (name c,o,n)

  8. Now load your data onto your selection using the data2b_atom function defined within data2bfactor.py.

    PyMOL> data2b_atom MyMethyls, /Users/username/Documents/datafile.txt

  9. Apply the color gradient:

    PyMOL> spectrumany b, red yellow, methyls
  10. Ray trace, save the image!