Dear Monica, for refmac5 this is nicely explained at http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Occupancy
Best, Tim On 03/11/2014 12:14 PM, Monica Mittal wrote: > Dear Sir > May i know how to refine the group occupancy for a ligand??? > > Thanx in advance > > On Mon, Mar 10, 2014 at 2:11 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. > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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