The map doesn't look good. What is the contour level for these maps?
As Tim suggested, you should try rebuilding the model.
Besides using the softwares which are listed by Tim, you can use
AutoRickshaw server for structure determination.
Do the rest of the regions (excluding the ones you've shown in the image)
look the same as those in these images?
If yes, then probably you should consider reprocessing the data in
different space group.
On Thu, Dec 1, 2016 at 7:48 PM, Tim Gruene <tim.gru...@psi.ch> wrote:
> Dear V,
> your map still looks quite poor and disconnected. Maybe you could improve
> overall model before you worry about such detailed questions like main
> vs. side chain density.
> If your resolution is not too poor, you could try rebuilding your model
> shelxe, or buccanner, or phenix, or ...
> On Thursday, December 01, 2016 02:35:21 PM Veronica Fiorentino wrote:
> > Dear bb-ers,
> > Is it uncommon to see side-chains for PHE/ARG visible in density but the
> > main-chain density breaking (say within a beta-strand)? I have attached
> > 1.FEM (map) 2&3. Experimental phase map. If I refine the model as
> > the side-chains appear green in difference map. I therefore assume that
> > sequence assignments are correct(?). Is this symptomatic of some big
> > mistake?
> > R/Rfree are around 27/32 % respectively. The phase problem was solved by
> > SeMet phasing.
> > Many thanks
> > V[image: Inline images 1]
> > [image: Inline images 2]
> > [image: Inline images 3]
> Paul Scherrer Institut
> Dr. Tim Gruene
> - persoenlich -
> Principal Investigator
> Biology and Chemistry
> CH-5232 Villigen PSI
> Phone: +41 (0)56 310 5297
> GPG Key ID = A46BEE1A
Tushar B. Raskar
Project JRF (DBT),
Protein Crystallography Lab,
Department of Biosciences and Bioengineering,
Indian Institute of Technology - Bombay.