By the way, I would recommend running simulated annealing with each composite omit map you generate to help in overcoming model bias.
-Daniel On Sat, Nov 10, 2018 at 9:31 PM Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> 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> > 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
