[modeller_usage] Re: Adding loops to X-Ray

[Modeller Caretaker <>]

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
-- 
             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage