Hello Eleanor, The resolution was 2.7 A and final R/Rfree = 19/23 The model was complete. water molecules were added. The green elongated density was present at the periphery of the protein.
Regards Amlan On Tue, Mar 11, 2014 at 6:53 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk>wrote: > You dont say what resolution you are working at, or what the current R > factor is. or how complete the model is. > > There are assumptions made in the refinement scaling algorithms and in > their treatment of supposedly poorly ordered solvent which can generate > false density (both positive and negative) on the boundaries of the model. > > And as well as Herman says the Sigma level is set globally whereas the > actual density locally is affected by the B values. One of the strengths of > COOT is that it is easy to adjust the sigma level at local regions. > Eleanor > > > > > > > On 11 March 2014 07:42, Amlan Roychowdhury <amlan.iit...@gmail.com> wrote: > >> Dear All, >> >> Thank you very much for your reply. >> I have an another doubt and I want to discuss with you. >> >> Sometimes for some structure during refinement and model building we have >> found a green blob (Fo-Fc and >5 sigma). >> If I scroll down the blue 2Fo-Fc map to a very low sigma level nearly at >> 0.5 a really non convincing density will appear. >> And from the structural point of view, it will be very difficult to put >> anything within it due to its position within the structure. >> as an example once I have found an elongated green density without any >> trace of blue in between a helix and a beta sheet. >> >> Is it due to noise? The structure was well refined. >> What should we do in such cases? >> >> Regards >> amlan. >> >> >> >> On Mon, Mar 10, 2014 at 4:41 PM, <herman.schreu...@sanofi.com> wrote: >> >>> Dear Amlan, >>> >>> >>> >>> The sigma of an Fo-Fc map map depends on the residual noise in your map. >>> In a well-refined structure, the sigma will be low, so at 3 sigma it will >>> show very weak features. >>> >>> My guess is that your ligand is present in partial occupancy and that >>> you will find it in your 2Fo-Fc map when you scroll down your contour >>> level. If you see convincing Fo-Fc density without a ligand being fitted, >>> the presence of the ligand must be real and you can fit it. However, I >>> would refine a group occupancy for your ligand. >>> >>> >>> >>> Best, >>> >>> Herman >>> >>> >>> >>> >>> >>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag >>> von *Amlan Roychowdhury >>> *Gesendet:* Montag, 10. März 2014 09:09 >>> *An:* CCP4BB@JISCMAIL.AC.UK >>> *Betreff:* [ccp4bb] regarding Fo-Fc map in coot >>> >>> >>> >>> Dear All, >>> >>> Some times during model building in coot we have found that at the >>> position of ligand molecules and water, there is a good Fo-Fc map (above 3 >>> sigma), devoid of any 2Fo-Fc map. >>> >>> 1.What does it physically mean and why the 2Fo-Fc map was not generated >>> properly? >>> >>> >>> >>> 2. Can we fit ligand molecule there? >>> >>> Thanks in advance. >>> >>> Best Wishes >>> >>> Amlan. >>> >>> >>> >>> -- >>> Amlan Roychowdhury. >>> Senior Research Fellow. >>> Protein Crystallography Lab. >>> Dept. of Biotechnology, >>> IIT Kharagpur. >>> Kharagpur 721302 >>> West Bengal. >>> India. >>> >> >> >> >> -- >> Amlan Roychowdhury. >> Senior Research Fellow. >> Protein Crystallography Lab. >> Dept. of Biotechnology, >> IIT Kharagpur. >> Kharagpur 721302 >> West Bengal. >> India. >> > > -- Amlan Roychowdhury. Senior Research Fellow. Protein Crystallography Lab. Dept. of Biotechnology, IIT Kharagpur. Kharagpur 721302 West Bengal. India.
