Hello,
I am trying to create docking poses using D110_DNA_interface.py. For my application I do not need extremely accurate poses (RMSD<0.5) to be created, is there anyway to limit the number of cycles the scripts runs through to create a pose? Ideally, I want to create poses in the range of RMSD between 1-20 angstroms.
I tried using the "Custom docking" commands in the same sample script to change the number of cycles but get the following error:
AttributeError: 'DockMCMCycle' object has no attribute 'get'.
Thank you!
Category:
Post Situation:
With the DockMCMProtocol object there are a few options you can change to change how extensively it samples: http://graylab.jhu.edu/PyRosetta.documentation/rosetta.protocols.docking.html#DockMCMProtocol
In particular, you can use the set_first_cycle() and set_second_cycle() methods to adjust the number of cycles of the DockMCMCycle mover. The defaults are 4 and 45, respectively.
There's also some setup and post-docking minimization steps which are done. If you're uninterested in this, you can simply use the DockMCMCycle mover directly. (This is what the "Custom Docking" section is doing.) . .. You may need to call dock_mcm.init_mc(pose) before running it.
I'm not quite sure why you're getting the error with "get" - what's the exact command that's being run before that error? (You may want to manually step through the protocol on the interactive terminal to see where it happens.)