Sorry, the R-factor gap of no6 is 5.23%, not 6.23%, I have made a mistake.
I have check the b-factor of the residue with "B-factor variance" value of 417
in coot-->menu-->distance-->residue info., the b-factor value of each atom of
the residue is very similar with that of in pdb file, though not exactly the
same. In addition, among the residues with high "B-factor variance" , some are
fitting quite well into the density, but some have very poor density for side
chain. It seems that "B-factor variance" and b-factor doesn't mean the same
thing. I still don't know what's the "B-factor variance" stands for?
Moreover, if density is missing for residue side, I would like to pick an
appropriate rotamer and let the b-factors rise to account for disorder.
I really appreciate your advice.
At 2017-05-04 19:45:14, "Vipul Panchal" <panchal.vi...@igib.in> wrote:
1) the difference is 5.23 % and it is good and acceptable.
2) if higher value belongs to residue, then you need to change the rotamer
Using coot , follow menu-->distance-->residue info. You will get to know to
whom 417 B factor value belongs. Meanwhile, just check if modeled residue or
part of residue has relevant density. If density is missing for part of
residue, then set occupancy to zero for the relevant atom(s). If density is
missing for the model of residue, then just remove side chain. I would
recommend to check density fit (coot-->menu--> validate--> density fit) for all
residues with >50 B factor value (coot-->menu--> validate--> temp. fact.
variance analysis).
On 04-May-2017 3:26 PM, "yanqiaoling2782048" <yanqiaoling2782...@126.com> wrote:
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
