[PyMOL] 2 proteins plus ligand

Hello, Like others, I am new to Pymol. I am interested in seeing if a small molecule (.mol2) "ligand" has a binding site on one of two proteins (2KAV and 5FEB) but since they are known to interact, it might be something between the two. While I am also looking into/learning Autodock Vina, in Pymo

Re: [PyMOL] 2 proteins plus ligand

Hi Larry, My guess is that you need a docking tool (like DOCKTHOR server; https://dockthor.lncc.br/v2/). So you pulled the protein structures from the web... the coordinates from one is arbitrary to the other. If they interact in a way that forms a protein-protein interface (PPI) then you need a

Re: [PyMOL] cmd.get_fastastr()

I used the function to check if the fasta is smaller than 25 characters. If it is then it is a peptide: https://github.com/pslacerda/pymol-labimm/blob/master/scripts/peptbase/create.py#L186 There is another way to check for peptides using only selection? Em seg., 6 de jul. de 2020 às 02:47, Thoma