I am trying to build a model of a 6 Da protein from the diffraction data
collected at 2.0 A resolution. There is a 10-residue stretch that has such bad
electron density that even at 0.4 sigma level one can hardly see any well
defined density for residues with long side chains.
My question
Thank you Afonine, Hans, Kumar, Deliang, Mark, Jose, Tim, Eleanor and Ed for
sharing your thoughts.
Here is a summary of the responses I received-
1. One should try to model residues based on 2Fo-Fc maps contoured at 1.0 sigma
level. Structures of mobile regions/loops can sometimes be modeled
I am currently trying to refine a structure where a 5 residue stretch of a
chain is in 2 conformations. Oddly enough, 1 of these 5 residues is in dual
conformations in both the conformations! Is there a conventional nomenclature
for defining such dual-dual conformations?
Refmac5 does not accept
I am told by a mentor that rigid body refinement should never be the last
refinement before submission to pdb. Any idea why? Structures in which every
round of retrained refinement messes up a conformation, is there any
alternative to not using rigid body refinement?
Andy
Thank you for your responses.
Restrained refinement does a good job at refining most of the structure except
a small region with poor density. Every time I refine it, it puts this region
completely out of the map. It doesn't have much effect on overall geometrical
factors as its a very small pa
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
dif
