Many molecule viewers allow you to color protein structures according to the value in the B-factor column of the pdb file (columns 61-66). PyMOL offers the "spectrum" command as a way to flexibly color your object, both atoms and surface, as well as the possibility for scripting on the fly replacement of B-factors or by values calculated "on the fly", e.g. proximity to a ligand or to the centre of gravity of the molecule ( see https://pymolwiki.org/index.php/Color , https://pymolwiki.org/index.php/Advanced_Coloring , https://pymolwiki.org/index.php/Spectrum , https://pymolwiki.org/index.php/Ramp_New )

Try "Bio3D" in R

load your pdb file read.pdb( ) function, each atomic cordinates x,y,z will consider as separate columns . By default your data will be a data frame. Covert your data frame into a matrix. From matrix you can generate the heatmap. You may choose any colour based on +ve and -ve values.

here are some ref

https://cran.r-project.org/web/packages/bio3d/index.html

http://rstudio-pubs-static.s3.amazonaws.com/10585_1a1fb580a417465cb00cb0238e13e59e.html

Dear Alexander Supertramp

These links might be an valuable asset, have a look:

1. https://chartio.com/learn/charts/heatmap-complete-guide/

2. https://www.biostars.org/p/8281/

3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489527/

4. https://towardsdatascience.com/all-about-heatmaps-bb7d97f099d7

Kind Regards

Qamar Ul Islam