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? I did not see this methodology amongst the Modeller tutorials but think it is best to maintain the fidelity of the protein as a whole i.e. non-stitching.
Thanks:) Joel
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
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Joel Subach -
Modeller Caretaker