On 8/13/20 7:24 AM, Joel Subach wrote: > Hi I want to build a C and N tail and one cytoplasmic loop that are > missing from the PDB Cryo-EM 3-D coordinate file of a transmembrane > protein. These regions were too dynamic during their Cryo-EM process > and therefore are left out of the structural file that the investigators > input into the PDB. Is there a way to model just these missing tails > and one loop WITH the rest of the protein meaning not modeling the > regions separately and then stitching them into the existing PDB > coordinate file subsequently?
Of course, just use the original PDB as your template and the full sequence, including the C and N tails plus the loop, as your target. Override select_atoms() if you don't want the original PDB residues to move. This is very similar to the "missing residues" example in the wiki: https://salilab.org/modeller/wiki/Missing%20residues
Ben Webb, Modeller Caretaker