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Changing the Number of Cycles of Script

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Changing the Number of Cycles of Script


I am trying to create docking poses using  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!

Post Situation: 
Mon, 2016-10-24 11:33

With the DockMCMProtocol object there are a few options you can change to change how extensively it samples:

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.)




Mon, 2016-11-14 13:56