Dear Rohit Kumar Singh, you can remove a couple of residues before and after the outlier and rebuild it. You can also switch on Ramachandran restraints in Coot and run real-space refinement. If this does not help, I would delete a single residue within the region in question, run real-space refinement for both segments and reconnect.
Regards, Tim On 01/13/2015 08:35 AM, rohit kumar wrote: > Hello all, > > if outlier is in between 5 to 6 %, how someone can fix it. > As the resolution is low (3.0-3.5 A). > > On Mon, Jan 12, 2015 at 7:53 PM, Robbie P. Joosten <[email protected]> wrote: > >> Hi Dialing, >> >> 86% favoured can actually be quite okay for an initial model. As long as >> it doesn't have 14% in the disallowed region, the vast majority of residues >> will be correct, or close enough to the correct answer that they can be >> fixed easily. Of course, such a model will need tweaking, but this is more >> or less the point of calling it an 'initial' model. >> >> Cheers, >> Robbie >> >> >> On 01/12/2015 01:18 PM, Dialing Pretty wrote: >> >>> Dear All， >>> >>> If an initial PDB has only 86% residues in the Ramachandran favored >>> region, it >>> would mean there is a significant error (for example significant length of >>> protein fragment in the total protein assigned to the wrong electron >>> density map >>> position) , right? >>> >>> Dialing >>> >>> > > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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