Did I miss a follow-up letter with more information? All I've seen is that Dr. Anandan said that there was a model based on 2.65 A resolution data with an average B factor of 82 A^2. Does this fact alone call for weeks of work attempting to remove model bias? Dr. Anandan didn't even say this structure was solved via molecular replacement. No indication of high R factor or stuck refinement. No details at all. Just a model with a fairly reasonable, if somewhat low, average B factor.
Dale Tronrud On 11/10/2018 6:31 PM, Daniel M. Himmel, Ph. D. wrote: > Anandhi, > > Assuming the data reduction went well, and you're in the right space goup, > there could be a lot of model bias in your structure stemming from the > starting model. > > There are a lot of things to try. I would > set all the B-factors to an artificially low B-factor to help de-mask > errors. Then, > you can generate a composite omit map and FEM maps to see if any obvious > model errors show up in the electron density. After correcting these, > you can try running > Autobuild and PhaseAndBuild in Phenix. Compare all the models you get from > each of these, especially in regions where your original model had high > b-factors. > Use Coot to identify areas of poor agreement with electron density and areas > of poor geometry. Once you spent a while correcting the model, put it > through > one or more cycles of simulated annealing at different temperatures in > parallel. > Select several sets of coordinates that give the best Rfree convergence, > and then > subject those models to individual B-factor refinement. After that, > check again in Coot > for areas of high B-factors and areas of poor geometry (try especially > to improve > your Ramachandran Plot). Use MolProbity to help in identifying errors > and clashes. > If a few rounds of simulated annealing and model building don't improve > things, try some > refinement in CCP4 Refmac. PDB_REDO, which uses Refmac, can also help > give you alternative models. While doing all these, don't be afraid to > "cut-and-paste" > regions from one model into another model and then correct the geometry > in Coot. > If B-factors don't come down no matter what you do, you could be in the > wrong space > group or have problems with the original data that need to be addressed. > > I hope this helps. > > Daniel > > ___________ > > Daniel M. Himmel, Ph. D. > > URL: http://www.DanielMHimmel.com/index_Xtal.html > <http://www.danielmhimmel.com/> > > > > > On Thu, Nov 8, 2018 at 7:41 PM Anandhi Anandan > <anandhi.anan...@uwa.edu.au <mailto:anandhi.anan...@uwa.edu.au>> wrote: > > Hello everyone, > > > I am trying to solve the structure of a protein with a bound ligand > at 2.65 A resolution. XDS was used for data reduction, phaser-MR for > molecular replacement and Phenix for refinement. The refinement was > done with the default settings ( individual B factors, occupancy and > TLS parameters). The resultant atomic B factors are quite high. The > overall B factor is 82 with a minimum value of 34.57 and maximum of > 225.13. I would like to know if any of the data reduction parameters > can affect the B factors and how best to deal with this issue. > > > Anandhi > > > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
