Hi, I have a question after readng this. What command should I use to do Cartesian or torsion-angle simulated annealing? Where should I change if I want to run .eff? } simulated_annealing { start_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 25 time_step = 0.0005 n_print = 100 update_grads_shift = 0.3 refine_sites = True refine_adp = False max_number_of_iterations = 25 mode = every_macro_cycle *second_and_before_last once first verbose = -1 Thanks for the answer. PC
From: [email protected] Date: Tue, 8 Dec 2009 12:34:09 -0800 To: [email protected] Subject: Re: [phenixbb] refinement
I do have very low resolution data (around 4 ang), what are the efficient way of doing refinement, either rigid body alone or rigidbody and tls or individual with group_adp. I did both, but not much significant changes in Rfree stays around 48/50%.
You could also try Cartesian or torsion-angle simulated annealing. I'd try both. In my experience Cartesian SA often works better even at low resolution. If you get errors running torsion-angle annealing, please try the latest nightly build (dev-249) since I've fixed several problems since the 1.5-2 release.
Also I do have other questions
1. While doing rigid body refinement, phenix complaint about the special position and could not perform rigid body refinement, whereas individual site refinement is working fine. I do have to delete the atom in special position for rigid body refinement?
You could use sites.rigid_body = ... to select the bodies you want to refine. The rest (including your atom on the special position) will not move.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_________________________________________________________________ Keep your friends updated—even when you’re not signed in. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/soc...