Hi, 1> Well, it seems you are just comparing Max value across all protocols. You should compare average values as it also takes into account no. of atoms with given values of B factor. As per refinement results, it seems though no. 6 has highest B factor value, number of atomic outliers are relatively low. So if you ask me no. 6 is the best one. Coot results are also in congruent with refinement results. I think you should go ahead with no.6 strategy.
2> When comparing B factor values of 417 vs 76, you should consider what it belongs to. As i may guess, 417 value belongs to an atom of residue whereas 76 belongs to residue. Meaning 417 is individual B factor whereas 76 is grouped B factor. On Thu, May 4, 2017 at 9:08 AM, yanqiaoling2782048 < yanqiaoling2782...@126.com> wrote: > Dear all, > > I'm working on a crystal structure with resolution of 2.2A. At the final > step, I use different strategies to refine the structure, they are: > no4: strategy=individual_sites+individual_adp+tls / set_b_iso=20 > results: Rwork/free=0.2052/0.2658 b-factor=11.4/136.8/48(min/max/average) > > no5: strategy=individual_sites+individual_adp+tls / set_b_iso=10 / > optimize_xyz/adp_weight=true > results: Rwork/free=0.2161/0.2639 b-factor=11.3/135.2/48.4(min/ > max/average) > > no6: strategy=individual_sites+individual_adp / anisotropic for all > residues and isotropic for water / > set_b_iso=10 / optimize_xyz/adp_weight=true > results: Rwork/free=0.2183/0.2706 b-factor=10.9/144.6/45.7 > (min/max/average) > PS: the results is read from pdb file > > The results showed that the strategy of no5 is the best one. But the "B > factor variance Graphs" generated by coot with > menu/validate/temp.fact.variance > analysis, have shown that no6 have the lowest B-factors (the attached > figure is the B-factor graphs of three pdb files). And my questions are: > 1. Which strategy should I choose to refine my structure? Or any other > suggestions to refine the structure at 2.2A resolution? > 2. Does it possible that some residues have very high B-factor in "B > factor variance Graphs", while in the pdb fileļ¼ the b-factor of > corresponding residues are relatively low? For example, one residue have > B-factors of 417 in "B factor variance Graphs", but in PDB file the b > factor is 76. Does the two factor mean the same thing? > 3. If i want to set the weight manually, which parameter should i set, > wxc/wxc_scale? or others? > > Thanks in advance. > > Best regards, > Qiaoling Yan > > > > > -- Vipul Panchal Senior Research Fellow, Respiratory disease and biology, CSIR-IGIB (M)-9540113372
