On 1 September 2013 11:31, Frank von Delft frank.vonde...@sgc.ox.ac.ukwrote:
2.
I'm struck by how small the improvements in R/Rfree are in Diederichs
Karplus (ActaD 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/);
the authors don't discuss it, but what's current thinking on how
Hi Frank and Ian,
We struggled with the small changes in free R-factors when we implementing
the paired refinement for resolution cut-offs in PDB_REDO. It's not just the
lack of a proper test of significance for (weighted) R-factor changes, it's
also a more philosophical problem. When should you
:* Tuesday, August 27, 2013 7:45 AM
*To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Resolution, R factors and data quality
Hi all,
does this not again bring up the still prevailing adherence to R
factors and not a shift to correlation coefficients ( CC1/2 and CC
On 1 September 2013 11:31, Frank von Delft frank.vonde...@sgc.ox.ac.ukwrote:
2.
I'm struck by how small the improvements in R/Rfree are in Diederichs
Karplus (ActaD 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/);
the authors don't discuss it, but what's current thinking on how
Hi Bernhard,
snip
But the real objective is – where do data stop making an improvement to the
model. The categorical statement that all data is good
is simply not true in practice. It is probably specific to each data set
refinement, and as long as we do not always run paired refinement
: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Arka Chakraborty
[arko.chakrabort...@gmail.com]
Sent: Tuesday, August 27, 2013 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data quality
Hi all,
does this not again bring up the still prevailing
7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data quality
Hi all,
does this not again bring up the still prevailing adherence to R factors and
not a shift to correlation coefficients ( CC1/2 and CC*) ? (as Dr. Phil
Evans has indicated).?
The way we
.
** **
Jim
** **
--
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Arka
Chakraborty [arko.chakrabort...@gmail.com]
*Sent:* Tuesday, August 27, 2013 7:45 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Resolution, R factors and data
and I am sure they
will ask me again.
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Arka
Chakraborty [arko.chakrabort...@gmail.com]
Sent: Tuesday, August 27, 2013 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data
We don't currently have a really good measure of that point where adding
the extra shell of data adds significant information
so it probably isn't something to agonise over too much. K D's paired
refinement may be useful though.
That seems to be a correct assessment of the situation and a
What a statement !
Give reviewers maps, I agree however, what if the reviewer has no clue of these
things we call structures ? I think for those people table 1 might still
provide some justification. I would argue it should go into the supplement at
least.
Jürgen
Sent from my iPad
On Aug
Hi,
a random thought: the data resolution, d_min_actual, can be thought of as
such that maximizes the correlation (*) between the synthesis calculated
using your data and an equivalent Fmodel synthesis calculated using
complete set of Miller indices in d_min_actual-inf resolution range, where
what if the reviewer has no clue of these things we call structures ? I think
for those people table 1 might still provide some justification.
Someone who knows little about structures probably won’t appreciate the
technical details in Table 1 either
J rgen
Sent from my iPad
On Aug
Jim,
This is coming from someone who just got enlightened a few weeks ago on
resolution cut-offs.
I am asked often: What value of CC1/2 should I cut my resolution at?
The KD paper mentioned that the CC(1/2) criterion loses its significance at ~9
according to student test.
I doubt that this
Excellent point about R-factors. Indeed, at this resolution they should be
quite lower than what you have. Did you:
- model solvent?
- use anisotropic ADPs?
- add H (this alone can drop R by 1-2%)?
- model alternative conformations?
- How R-factors (Rwork) look in resolution?
Pavel
On Mon, Aug
limits for cut-off of
(reasonably complete) high resolution shells.
LG, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Emily
Golden
Sent: Dienstag, 27. August 2013 07:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data quality
Thanks
The question you should ask yourself is why would omitting data improve my
model?
Phil
On 27 Aug 2013, at 02:49, Emily Golden 10417...@student.uwa.edu.au wrote:
Hi All,
I have collected diffraction images to 1 Angstrom resolution to the edge of
the detector and 0.9A to the corner.I
Hi all,
does this not again bring up the still prevailing adherence to R factors
and not a shift to correlation coefficients ( CC1/2 and CC*) ? (as Dr.
Phil Evans has indicated).?
The way we look at data quality ( by we I mean the end users ) needs to
be altered, I guess.
best,
Arka Chakraborty
of Arka Chakraborty
[arko.chakrabort...@gmail.com]
Sent: Tuesday, August 27, 2013 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data quality
Hi all,
does this not again bring up the still prevailing adherence to R factors and
not a shift to correlation
@JISCMAIL.AC.UK]
on behalf of Arka Chakraborty
[arko.chakrabort...@gmail.commailto:arko.chakrabort...@gmail.com]
Sent: Tuesday, August 27, 2013 7:45 AM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data quality
Hi all,
does this not again bring up
[CCP4BB@JISCMAIL.AC.UK] on behalf of Arka
Chakraborty [arko.chakrabort...@gmail.com]
Sent: Tuesday, August 27, 2013 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Resolution, R factors and data quality
Hi all,
does this not again bring up the still prevailing adherence to R factors
Hi All,
I have collected diffraction images to 1 Angstrom resolution to the edge of
the detector and 0.9A to the corner.I collected two sets, one for low
resolution reflections and one for high resolution reflections.
I get 100% completeness above 1A and 41% completeness in the 0.9A-0.95A
Hi Emily,
I get 100% completeness above 1A and 41% completeness in the 0.9A-0.95A
shell.
However, my Rmerge in the highest shelll is not good, ~80%.
The Rfree is 0.17 and Rwork is 0.16 but the maps look very good. If I
cut the data to 1 Angstrom the R factors improve but I feel the maps
Thanks Yuriy and Pavel,
at this resolution one would expect R/Rfree to be ~ 10-11%/12-13% assuming
you applied anisotropic B-factor refinement ( and probably having a low
symmetry SG).
R merge of 80% may be OK if I/sig for high res shell is 2.
Yes, I used anisotropic Bfactors and the space
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