I have some very basic questions about model refinement process.
1. Why Refmac5 refinement from Coot GUI gives different results than Refmac5
refinement from CCP4i? One obvious difference is that COOT refinements are
local whereas CCP4i refinements are global. But why should it make a major
difference?
2. Is it acceptable to deposit a model to PDB which has been last refined using
Refmac5 from within COOT GUI?
3. Which cases warrant use of TLS and NCS restraints? When is it most
appropriate to use anisotropic refinement?
4. PHENIX permits defining different refinement strategies for different parts
of the structure. Can a structure part of which has been rigid body refined in
the last step, be deposited to PDB?
5. How to prevent Refmac from introducing close contacts during refinement?
Setting up geometric parameters (Distance restraint overall wt 1.0) does not
seem to be of any help.
Thanks!
AM
