I also should backtrack a little. I assumed that Anandhi has good
data reduction with good statistics, no data problems (such as twinning),
a good molecular replacement solution, and refinement stuck, but he
didn't give any of those details. What are the R and Rfree values, the RMS
bonds & angles
Okay, I'm an idiot. The letter did say molecular replacement. I
have no excuse for being so blind.
I do stand by my statement: I don't see that an average B factor of
82 A^2, by itself, indicates any serious problem with a model at 2.65 A
resolution.
I have generally found that the ave
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
Hard to comment on PHEIX refne but check these things: such results must
either mean your molecular replacement solution is wrong or there is
something wrong with the data.
Refinement packages will always try to match the Mean B factor to the
Wilson plot B so I think the problem must be before refi
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'
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
Dear Anandhi,
you might be interested in PMID: 29752562.
BW,
Oliviero
On 09.11.2018 01:30, Anandhi Anandan 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 a
Hi,
The "B factors" reflect the rapidity of the decrease in intensity of
scattering with increasing resolution. The scattering of a crystal
becomes unmeasurable at a lower resolution if its intensities drop
faster. This results in a connection between the resolution of a data
set and the aver
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
bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> > Matthias Barone [bar...@fmp-berlin.de]
> > *Sent:* Friday, October 14, 2016 8:00 AM
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor
> >
> > Picking up the mail of Pavel,
-
> > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> > Matthias Barone [bar...@fmp-berlin.de]
> > *Sent:* Friday, October 14, 2016 8:00 AM
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* [ccp4bb] Ant
oms ...
Carlos
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Matthias Barone [bar...@fmp-berlin.de]
*Sent:* Friday, October 14, 2016 8:00 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor
, but they'll never think to color it by occupancy.
>
> --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthias
> Barone [bar...@fmp-berlin.de]
> *Sent:* Friday, October 14, 2016 8:00 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Antw:
tw: Re: [ccp4bb] High B factor
Picking up the mail of Pavel, Phenix refines occupancies..
If you expect the loops to be disordered, did you try to lower the occupancy of
these residues, following Ethan Merritt statement that "general uncertainty
[...] is represented better by occupancy <1 r
I agree that it would certainly be bad if your model was inconsistent
with the Wilson B. When I first ran into people who were worried about
this I recommended that they calculate the Wilson B of their model, not
look at the average B as a proxy. You can calculate structure factors
from your
Picking up the mail of Pavel, Phenix refines occupancies..
If you expect the loops to be disordered, did you try to lower the
occupancy of these residues, following Ethan Merritt statement that
"general uncertainty [...] is represented better by occupancy <1
rather than an arbitrary large B fact
> If you are still worry about your Bfactor, you could try TLS,
>
Or NCS, but SA with MLHL might be better.
(A joke).
Sunanda,
As "common people", ... "agreement" don't means for me "equals" ...
So I hope I'm not so "incorrect" if I keep one mind the Wilson B as the
model
refinement goes and the average B factor changes with different strategies.
If you are still worry about your Bfactor, you could try TLS,
It seems to be common for people to make the incorrect assumption
that the average of the atomic B factors in the PDB file should equal
the Wilson B. The Wilson B is actually a weighted average of the
individual B factors where the weighting is rather mysterious, but the
small B factors have m
Sorry for not making the problem clear!
The overall B factor for the 3.0 A structure is around 98.00 A*2. Most of
the deposited structures in the PDB site around this resolution
has an av B around 70 A*2
All other statistics looks fine. I got a warning message while trying to
upload the structu
Hi Sunanda
They don't need to be "better" ... they need to be in agreement with you
experimental B factor ... Wilson plot?
Best
Carlos
On 10/13/16 04:59, sunanda williams wrote:
Hi all,
I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is
around 98. The B value is especial
I fully agree with Dale in not understanding what the problem is. Perhaps I
have a better chance if you clearly explain what exactly you mean by "is
there any way to better the B factors".
Pavel
On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud
wrote:
>I'm sorry but I don't understand what your
.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: [ccp4bb] High B factor
Hi all,
I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is
around 98. The B value is especially high at the N terminus and two loop
regions (around 120-150 AA).
The rest of the structure averaged around 70-75. Has
I'm sorry but I don't understand what your problem is. Do you think
the B factors are too small for a 3A data set? A range of 70 to 75 is a
little smaller than usual but probably not out of bounds.
Dale Tronrud
On 10/12/2016 7:59 PM, sunanda williams wrote:
> Hi all,
> I have a structure at
Hi all,
I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is
around 98. The B value is especially high at the N terminus and two loop
regions (around 120-150 AA).
The rest of the structure averaged around 70-75. Has anyone faced such a
scenario? How reliable is the structure and is
inal Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> ka...@ssl.serc.iisc.ernet.in
> Sent: Wednesday, May 11, 2011 12:00 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] High B-factor for metal
>
> Dear Sir,
>
> The resolution is 2.35
ay, May 11, 2011 11:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] High B-factor for metal
Dear users,
I have refined a structure in R3 with cadmium bound to it, which was present in the
crystallization condition. There are 2 chains in the asu. The structure is twinned. R and
Rfree is a
: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
ka...@ssl.serc.iisc.ernet.in
Sent: Wednesday, May 11, 2011 12:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] High B-factor for metal
Dear Sir,
The resolution is 2.35Ang. I was trying to refine Cadmium occupancy using
the
On 05/11/2011 10:30 AM, ka...@ssl.serc.iisc.ernet.in wrote:
Dear users,
I have refined a structure in R3 with cadmium bound to it, which
was present in the crystallization condition. There are 2 chains
in the asu. The structure is twinned. R and Rfree is around 22% and
28%. One of the cadmiu
mate of the occupancy will be compensated by the Bfactor.
>
> Good luck,
> Herman
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> ka...@ssl.serc.iisc.ernet.in
> Sent: Wednesday, May 11, 2011 11:30 AM
> To: CCP4
et.in
Sent: Wednesday, May 11, 2011 11:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] High B-factor for metal
Dear users,
I have refined a structure in R3 with cadmium bound to it, which was present
in the crystallization condition. There are 2 chains in the asu. The structure
is twinned. R an
Dear users,
I have refined a structure in R3 with cadmium bound to it, which
was present in the crystallization condition. There are 2 chains
in the asu. The structure is twinned. R and Rfree is around 22% and
28%. One of the cadmium has extremely high B-factor of 127, I tried
replacing it with
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