Hi Vipul,
Thanks for your quick reply.
1. Actually, i mainly comparing the gap between Rwork and Rfree which should be
<5%, and then the overall b-factor, RMSD of bond and angle. For me, no5 is the
best one, but the "B factor variance Graphs" make me uncomfortable. The
R-factor gap of no6 is 6.23%, does this mean overfitting?
2. The b-factor value of 76 is belong to the atom of the residue obtained from
the pdb file. I'm not sure whether the B-factor in "B factor variance Graphs"
belong to residue or atom, but i guess 417 belongs to residue. What's the
relationship of the two factor?
Best regards,
Qiaoling Yan
At 2017-05-04 15:58:36, "Vipul Panchal" <panchal.vi...@igib.in> wrote:
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 is 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
