On 7/29/21 3:08 AM, Li Xue wrote: > Is it possible that we could track all the details of the modeller > conjugate gradients optimization process? For example, ask modeller at > each optimization step to output the PDB coordinates, modeller molpdf > energy terms and so on?

Certainly; see https://salilab.org/modeller/10.1/manual/node58.html and https://salilab.org/modeller/10.1/manual/node57.html

By default Modeller writes a trace file (e.g. 1fdx.D00000001) with energy values and other optimization statistics. If you also want coordinates or other information, you can set write_intermediates=True or override get_optimize_actions() to add additional optimizer actions such as WriteStructure (to write PDB files) or CHARMMTrajectory (to write a DCD trajectory).

Ben Webb, Modeller Caretaker