Hi Veronica, Yes, it is okay to exclude few residues or even short stretches of loops/helices/strands if there is no reliable/convincing electron density for them even at low map contours because if there is no convincing density you cannot reliably model the local structure.
However, if you refine with tight NCS, which you probably should do at this resolution unless there are significant differences in the 4 molecules, you can also choose to keep residues for which there is no reliable density in one of the molecules, provided those residues are well resolved in the other molecules and refine well (density, B-factors). Also use TLS refinement. Irrespective of which of the 2 options you choose, make sure to add a remark in the PDB header about the option chosen, so that others know what was done and if you write it up in a manuscript, describe it there as well. Best, Debanu Das. > On Jan 10, 2017, at 3:30 AM, V F <veronicapfiorent...@gmail.com> wrote: > > Dear all, > I have a model with 4 molecules in asu. One of the domains is poorly > ordered, weak density. Please see the screenshot with 2 panel (2 > chains side-by-side). My question: In the right panel: > 1. Should I delete residues 653- 655? > 2. Should the helix 689-702 be deleted? can I keep a few residues - > orphaned? Is there a specific rule for these types of data. > > The map was generated with Phenix/FEM contoured at 1.5 sigma. Data set > at 2.8A. Many thanks for your advise. > > I looked at many PDB models + density from EDS there are poorly > defined regions. My chemistry based group has no experience on > bio-structures. > Veronica > <FEM-at-1.5-sigma.png>
