On 6/16/23 1:16 AM, majort--- via modeller_usage wrote:> 1. How can I add C- and N-terminal residues? I couldn't find a way > to do this. This is no different from adding an insertion in the middle of the sequence. The complication for loop modeling is that if one end of the loop is free, as will happen at a terminus, the sampler is likely to find "loop" conformations where the loop extends out into space away from the rest of the protein (remember, Modeller does not model solvent or crystal contacts). More likely you want the loop to be packed with the rest of the protein. To attempt to do that, you would need to place the terminal residue manually and exclude it from your loop selection.
> 2. How can I select and write the pdb file for the lowest energy > model after creating a large number of models (i.e., as part of a pipeline)?
You can write a little bit of Python code to query the outputs. There's an example at https://salilab.org/modeller/10.4/manual/node31.html
Ben Webb, Modeller Caretaker