PyMOL: Mapping properties onto a structure - Electrostatic potential, conservation, hydrophobicity/polarity, ...

The spectrum command

Properties are typically mapped via the B-factor column onto a protein structure, usually represented in cartoon mode or as molecular surface. The most important command is:

spectrum B, palette, selection, minimum, maximum

palette is one of the following options, describing the color change from minimum to maximum:

selection specifies the atoms that will be colored by the B-factor, usually the C_α-atoms, as these define the color of the fold or of the molecular surface. However, if you aim to depict a property on individual atoms, such as the rmsd values of a ligand in an MD simulation below, this is also possible.

minimum and maximum define the range of values to which the color spectrum is extended. If you omit these values, the range is determined automatically as the lowest and highest value present. If these are extreme "outliers", it may be necessary to narrow the range of spectrum color change by specifying the minimum and maximum values.

Examples

Click on the images to see the full resolution image.

	Electrostatic potential of the Y2R receptor. The electrostatic potential is mapped onto the molecular surface of the Y2R receptor (PDB id 7yon). This image was created with APBS plugin of PyMOL as described here. Note that the potential in the central membrane region does not describe the physiological situation as the hydrophobic membrane was not part of the calculation. Instead the potential was generated for the receptor in water. It is also possible to generate the electrostatic potential at the molecular surface using a PyMOL function accessible via the object buttons: OB: 7yon: A: generate, vacuum electrostatics, protein contact potential. I assume that the calculation via APBS is more sophisticated and allows for better control of the parameters and the structure.
	Sequence conservation of the pancreatic peptide. Conservation scores were calculated with the ConSurf server. The pdb file was downloaded and the scores were mapped onto the cartoon representation via the following commands. High conservation is indicated in pink, intermediate in white and low conservation in cyan. The C-terminal residues binding into the Y2R pocket are conserved. The very C-terminal tyrosine residue (drawn in red here) was not correctly processed due to the "TYC" residue name. It should have been renamed to TYR before the ConSurf analysis. load 7yon_L_With_Conservation_Scores.pdb hide all show cartoon, chain L spectrum b, hotpink white aquamarine, chain L, -1.5, 1.5 orient chain L turn z, 90 util.performance(0) draw 350,800
	Sequence conservation of the orthosteric ligand binding pocket of the Y2 receptor. Conservation scores were calculated with the ConSurf server. The pdb file was downloaded and the scores were mapped onto the molecular surface. High conservation is indicated in pink, intermediate in white and low conservation in cyan. The commands are similar as in the example above, with the exception that the surface is shown and not the cartoon. The binding pocket is conserved  The cartoon representation is not so useful, as the buried residues in the core of the protein always have higher conservation scores than the residues on the protein surface, for structural reasons. By mapping
	Sequence conservation of the cytosolic interface of the Y2 receptor.
	Hydrophobicity of the molecular surface of the Y2 receptor. The hydrophobicity has been quantified according to Eisenberg et al. J. Mol. Biol. 179:125-142 (1984). Using the pymol python script color_h.py, which you also may download from here and save it to a directory on your computer, a new command color_h is defined, which colors the amino acids according to the Eisenberg hydrophobicity scale. Using color_h increasing hydrophobicity is indicated by red color. The script also defines color_h2, which colors from green (polar) to grey (hydrophobic). I would prefer to color hydrophobic regions yellow, one would need to modify the color definitions on color_h.py to achieve that. Syntax: color_h <selection>. set bg_rgb, white fetch 7yon remove not chain R hide all show surface, chain R orient chain R turn z, 90 run color_h.py color_h
	Hydrophobicity and charge of the molecular surface of the Y2 receptor.This figure was generated using a python script of Hagemans and van Belzen. Hydrophobic atoms are colored yellow, positively charged groups blue and negatively charged groups red. Look at the python script for further details or changing the colors, which is easy for this script. Syntax: color_yrb <selection>. set bg_rgb, white fetch 7yon remove not chain R hide all show surface, chain R orient chain R turn z, 90 run color_YRB.py color_yrb
	Mapping charge, polarity and hydrophobicity onto the molecular surface. In the following script, atoms are colored according to charge, polarity and hydrophobicity and the corresponding molecular surface is shown. As an alternative to the following pml script, one could modify the color_YRB.py script to define a command for the coloring steps. fetch 7yon remove not chain R or hydrogen hide all color white # hydrophobic color white, ele C+S # polar set_color c_polar, [1.0, 0.8, 0.0] color paleyellow, name C+O+N color c_polar, (resn SER and name OG) or (resn THR and name OG1) color c_polar, (resn ASN and name CG+OD1+ND2) or (resn GLN and name CD+OE1+NE2) color c_polar, resn HIS and (sidechain and not name CB) color c_polar, (resn TRP and name NE1) or (resn TYR and name OH) # positive charge color blue, (resn ARG and name NE+NH1+NH2+CZ) or (resn LYS and name NZ) # negative charge color red, (resn ASP and name CG+OD1+OD2) or (resn GLU and name CD+OE1+OE2) show surface
	Color an AlphaFold model according to pLDDT values: load hsG4dimer_a13c4_unrelaxed_rank_1_model_2.pdb, pdb1 set bg_rgb, white dss spectrum b, rainbow_rev show cartoon util.performance(0) orient turn x, 110 clip slab, 50

The following figure shows an example, where the atoms of a ligand are color-coded by the root-mean-square fluctuations of a  molecular dynamics simulation. Blue color indicates low rmsf values, i.e. low mobility, and red high rmsf values. In addition to the color-coding, the rmsf values (in Å) are also listed next to the atoms. The rmsf values were stored in the B-factor column and the spectrum command was used to achieve the color-coding.