Ngo Duc Tri wrote: > I used Modeller to model one protein and I want to modify some part > using BIOPOLYMER (Sybyl software). However, the pdb file don't have the > CONECT record. The structure cannot be viewed in BIOPOLYMER. > Can you tell me how to add the CONECT record to the model structure?
CONECT records are typically used only for HETATM contacts. Modeller generally doesn't know what the HETATM contacts are, so is unable to write these records. If you really need them, you will have to write them out manually.
Modeller certainly knows the connectivity of ATOM residues, but does not write this into PDB files because the PDB format does not require it. But you could certainly use write_psf() (see http://salilab.org/modeller/9v1/manual/node165.html) to write out the topology in PSF format if that's useful to you.
Ben Webb, Modeller Caretaker