Re: [modeller_usage] Modeller Model Building Inquiry using existing PDB cooridnates

[Modeller Caretaker <>]

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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