This looks to me like a good attempt for GraphEnt. Give it a shot and you might be positively surprised.
Jürgen Sent from my iPad On May 13, 2013, at 21:26, "Dale Tronrud" <det...@uoxray.uoregon.edu> wrote: > Sometimes a floppy bit of a protein is even more floppy in a > particular crystal form. Your maps do not appear to support your > model of a helix in this location. I would not build it unless > maps based on later refinement show something reasonable in the > omit map. (Of course if you leave out the helix, all your maps > will be omit maps.) > > It is quite common to submit models to the PDB that do not > contain all of the amino acids expected based on the sequence. > If you can't see where the chain goes you certainly can't be > expected to build it. > > Dale Tronrud > > On 05/13/2013 04:23 AM, atul kumar wrote: >> I have attached the map and omit map(after deleting helix) images. >> >> 2Fo-Fc(1 sigma) >> >> Fo-Fc(3sigma) >> >> On 5/13/13, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: >>> Hard to say without seeing the maps and experimenting. My first check would >>> be to set the NTD occupancies to 0.0 - refine the CTD alone, then look at >>> the maps in COOT. >>> >>> Or maybe let an automatic modelling building program such as Buccaneer try >>> to rebuild the NTD section, with starting phases from the CTD. >>> >>> Eleanor >>> >>> >>> >>> >>> On 13 May 2013 09:04, atul kumar <atulsingh21...@gmail.com> wrote: >>> >>>> Dear all, >>>> >>>> I have solved the structure of my protein by molecular replacement at >>>> 2.9A, with Rfactor and Rfree 18 and 22 respectively. Overall everything >>>> seems fine, its a two domain protein NTD and CTD, the NTD have high >>>> average >>>> B factor compared to CTD. A helix of NTD seems to be disordered, I tried >>>> different geometric weights but the refined structure does not seem to >>>> follow proper geometry for this helix. The B-factor of this helix is very >>>> high compared to overall B factor for NTD and omit map shows only some >>>> partial density in this region( off course not conclusive). All the >>>> homologous structure have helix in this region although with high >>>> B-factor. >>>> Should I submit the current pdb or need more refinement? >>>> >>>> thanks and regards >>>> >>>> Atul Kumar >>>> >>>
