WebThe format is the number of electrons followed by the charge sign, for example "1-" or "2+". You can edit the PDB file manually to add this, but we recommend using phenix.pdbtools: … WebFeb 16, 2015 · The phenix refine with the resolution at 1.58A is still far from satisfactory, now the R-factor and R-free values are like this: 1.58 A =0.3020/0.3320 1.58 A detwin=0.2619/0.2996.
(IUCr) Real-space refinement in PHENIX for cryo-EM and …
WebWe compared Rosetta-Phenix refinement (phenix.rosetta_ refine) to three different low-resolution refinement strategies. As a control, structures were refined for 20 cycles in phenix.refine, optimizing X-ray weight at each cycle. We also refined structures in CNS. 1. 4 WebThe Phenix RSR documentation contains a line that > reads "T = Tmap + weight * Trestraints"—if I'm understanding correctly > (?), this means a larger "weight" value should … thomas\u0027 first wife kathy
Use of knowledge-based restraints in phenix.refine to improve ...
WebJul 27, 2016 · 2. Methods. Phenix.refine (Afonine et al., 2012) optimizes a crystal structure via a series of repeated cycles. During each cycle a series of parameters of the user's choosing are optimized. These usually include the atomic coordinates and the isotropic atomic displacement parameters, but can also include, for example, … WebSep 29, 2013 · As a control, structures were refined for 20 cycles in phenix.refine, optimizing X-ray weight at each cycle. We also refined structures in CNS 14, using the DEN methodology (with full... WebApr 1, 2012 · phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large ... thomas\u0027 halloween adventures volume 2