Mar 2, 2016 · Assign color by B-factor. B-factor coloring can be done with the spectrum command. Example: spectrum b, blue_white_red, minimum=20, maximum=50 as cartoon …

Oct 22, 2019 · # color atoms based on their distance from a point # returns the length of the distance between atom A and atom B diff_len = lambda x, y: math. sqrt ((x [0]-y [0]) * (x [0]-y …

Oct 24, 2019 · PyMOL can easily reassign the B-Factors and color them, too. The following example will load a protein, set ALL it's B Factors to "0", read in a list of properties for each …

It is useful to color a protein based on the b-factors of its backbone atoms to see the segments of the protein that are most dynamic (or where the uncertainty in atom positions is the highest). …

Mar 9, 2023 · There are several simple ways to color pLDDT (predicted local distance difference test) values of the AlphaFold2 (AF2) structures. I am showing a few examples using either …

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 …

Aug 30, 2020 · I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns. After running …

color_b(selection='sel',ramp=0 or 1, rainbow=0 or 1, nbins=10) or. color_b selection='sel',ramp=0 or 1, rainbow=0 or 1, nbins=10. This function allows coloring of a selection as a function of B …

Sep 29, 2014 · If you want to see the “b-factor putty” view where the backbone is displayed as a tube with a diameter correlated to the b-factor of the structure, simply click the Action button of …

Oct 13, 2014 · Now color by B-factor. If you are lucky and the color gradient you want is already included in Pymol, you can use the function spectrum: PyMOL> spectrum b, rainbow, …