I would appreciate if you guys can help me. I am very new in proteomics world. I am looking for a way to better visualize PDB files. I understand there are programs in addition to what pdb website offers, but I was not able to find a way to what I would like to achieve. Specifically, I am looking for a way to visualize the protein structure and the ligand (Histone modifications, as an example) bound to it. Kinda like what is published in figure 4 of this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130114/
I would really appreciate your help.