On 12/12/22 9:03 PM, Ecem Güngör via Chimera-users wrote:
What I found on the Modeller website is that potentially all of the atoms in the final model could move since either AutoLoop or LoopModel will try to build a comparative model using the input PDB as a template. You can check this site <https://salilab.org/modeller/wiki/Missing_residues>for more.
You are misinterpreting that text. Comparative modeling (which is what is described at that URL) will optimize the entire model by default (although you can ask it not to). Loop modeling of a given input structure will only move the loop atoms: https://salilab.org/modeller/10.4/manual/node36.html Of course, if you do comparative modeling followed by loop refinement, all the atoms will move because of the comparative modeling step. (I had thought my answer when you asked about this a week ago on the Modeller mailing list addressed your question, but if anything wasn't clear, please let me know.) Ben -- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle