Hello everyone I have to analyze interactions of some compounds with particular focus on some specific atoms. I downloaded those compounds from pubchem but the carbon atom numbering is different from what I found from literature and previous research (when viewed from different visualization tools). So I manually drew the structures using ChemDraw but it also assigns different atom numbers to carbon. I edited those serial numbers in chemDraw and ChemBio3D Ultra and saved it in pdb format but when I viewed this pdb file in pymol, it displayed different atom numbers. I know which atom number I want to focus on but it is difficult for me to manually search that atom number for multiple compounds. For example my focus is carbon atom 11 but it is labelled as say C-16 in 3D structure. In short visualization tools label the carbon atoms differently from what I found in literature. Please help me how to get the desired atom numbering. Thanks in advance
