Hello,
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?
Best,
Li
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
-
Li Xue -
Modeller Caretaker