Hi Dr. Bernhard, I was actually confused because the baverage program in ccp4 gave average bfactor of 25.0 for the residue but coot is showing 150! Also its a high resolution structure(res 1.6 ang) and the density after refinement is lovely and does not indicate any disorder. So I was wandering if I am interpreting the temp factor variance plot in coot in a wrong way!
Regards ARKO On Sat, Apr 21, 2012 at 11:58 PM, Bernhard Rupp <[email protected]>wrote: > Don’t worry. High B-factor just means that the probability of the atoms > being at the specified coordinate position is low, for whatever reason.*** > * > > In most cases this is completely normal and often indicative of solvent > exposed surface residues, and a look at the electron density will**** > > show whether this uncertainty is due to absence of electron density or a > result of poor modeling. Remember that cranking up the B-factor is the*** > * > > ‘emergency exit’ for the refinement program if an atom is located at an > incorrect coordinate position from which it cannot be expelled (due to *** > * > > stereochemical restraints). **** > > ** ** > > BR**** > > ** ** > > *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of *Arka > Chakraborty > *Sent:* Saturday, April 21, 2012 11:14 AM > *To:* [email protected] > *Subject:* [ccp4bb] high temp factor in coot!**** > > ** ** > > Hi all, > > I have solved the structure of a decamer dna oligonucleotide. Analysis in > CCP4 using baverage shows acceptable(<30) avg b factors for all the > residues. However temperature factor variance analysis option in coot gives > a figure of 150 for one of the residues with a huge red bar. I would like > to ask how should this be interpreted? What exactly does the bfactor plot > in coot signify? > > Thanks in advance, > > ARKO > > -- **** > > *ARKA CHAKRABORTY***** > > *CAS in Crystallography and Biophysics***** > > *University of Madras***** > > *Chennai,India***** > > ** ** > -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*
