Hi Almudena, some graphic programs connect atoms based on distance only (draw a line between two atoms that represents the covalent bond). I suspect this is what PyMol does. Some may employ more information such as one encoded in Monomer Library CIF files. Some try to do both. I suspect this is what Coot does. However, none of the two can represent exactly what refinement program "thinks" of bonding because refinement programs may employ even more (often quite sophisticated) heuristics to decide what's bonded and what's not bonded and how, including user specified custom bonds. This is why not seeing a line between to seemingly bonded atoms in a graphic program does not necessarily mean that these atoms were not bonded during refinement. This is exactly the reason why phenix.refine, for example, outputs a *geo file that lists absolutely all restraints (bonds, angles, planes, etc etc) making it absolutely clear what was restrained and how, for each and every atom. I guess Shelxl ins files do the same.
Pavel On Wed, Feb 4, 2015 at 9:07 AM, Almudena Ponce Salvatierra < maps.fa...@gmail.com> wrote: > Dear all, > > does anyone know why if I open a pdb in pymol (that appears normal and > fully connected in coot) it appears as if it was broken into pieces? > > Thanks, > > Almudena. > > -- > Almudena Ponce-Salvatierra > Macromolecular crystallography and Nucleic acid chemistry > Max Planck Institute for Biophysical Chemistry > Am Fassberg 11 37077 Göttingen > Germany > >
