Re: [modeller_usage] can we keep track of the modeller optimization process

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
modeller-care@ucsf.edu             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage