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
