If you refined with REFMAC - I look at the log graph under R factor v resolution. The second plot isd <Fobs> v <Fcalc> - obviously they should overlap but sometimes they dont, indicating scaling problems!
What is yours like? On 11 March 2014 14:16, Amlan Roychowdhury <[email protected]> wrote: > 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 <[email protected] > > 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 <[email protected]>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, <[email protected]> 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:[email protected]] *Im Auftrag >>>> von *Amlan Roychowdhury >>>> *Gesendet:* Montag, 10. März 2014 09:09 >>>> *An:* [email protected] >>>> *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. >
