I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...
I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot ...
There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...