On Sun, Oct 18, 2009 at 10:00 AM, Shaun Lott s.l...@auckland.ac.nz wrote:
In my experience, DALI can be better than SSM at detecting distant
structural similarities.
this is interesting. Do you take into account that, in difference of DALI,
SSM
has a control on the remoteness of structural
Dear all
I have been refining my structure using refmac5 restrained refinement
and the model currently has an R-factor of 0.19. What is concerning me
is that there is quite a big discrepancy between the Rfree and the
R-factor, with the Rfree being around 0.27. Furthermore, after about 10
Hi Sylvia
You didn't make it clear on what basis you think the discrepancy between
R and Rfree is too big, since the Rfree you would expect to get if the
refinement were bias-free depends a lot on a number of factors such as
the resolution, the data completeness, what parameters you are refining,
Dear Sylvia,
The discrepancy is only 8% and that is acceptable (you may be able to
get the Rfree lower by changing the refinement program for the ultimate
rounds of refinement, or by using TLS refinement if you don't do that
already --- you don't mention what refinement program you are
Dear all,
what are the best criteria to say that one monomer is more constrained by
the packing than another? surfaces analyses by PISA? How to be sure that the
observed differences are significant?
Thanks in advance.
Cedric Bauvois
Hi Sylvia:
-Original Message-
From: Sylvia Fanucchi [mailto:sylvia.fanuc...@wits.ac.za]
Sent: 19 October 2009 15:06
To: Ian Tickle
Subject: RE: how to improve Rfree?
Hi Ian
Yes, sorry, admittedly this is the first time I'm doing this and I'm
not
sure of all the checks that
*If* you are using WEIGHT AUTO, check the RMSDbonds. You don't say what
your resolution is, but I assume it's in lower 2.0s. I've seen refmac5
in some cases produce somewhat unreasonable geometries (i.e.
RMSDbonds0.025A) at such medium resolution and accordingly, large
R/Rfree gap. If this is
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Does anyone already have the PDB-wide R/Rfree gap versus resolution data
(it does not seem that the PDB maintains one)?
Ed.
The friendly people in Uppsala has something here by the name Harry
Plotter: http://xray.bmc.uu.se/gerard/supmat/eds/plotter.html
This might be somewhat dated now.
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My resolution is 1.6A although I have cut it to 1.8A to bring the
R-factor down. I've been performing restrained refinement in refmac5
using the default settings. The solvent content is 40%
This sounds fundamentally wrong. Even the Rmerge reduction by cutting
resolution practice is
I agree. It cannot be said too often that the object of refinement is
not to minimise the R-factor!
( while I'm at it, freeR has nothing to do with model bias (which is
largely imaginary anyway, only a problem with low resolution molecular
replacement))
Phil
On 19 Oct 2009, at 17:07, Ed
Sorry, I gave the wrong link, the R/Rfree gap is reported here:
http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
Engin
On 10/19/09 9:13 AM, Ed Pozharski wrote:
Looks great, thanks. But it doesn't actually report R/Rfree gap, or am
I missing something?
Ed.
On Mon, 2009-10-19 at
Hi Sivia,
you say the resolution is 1.8A, and your R-work=0.19 and R-free=0.27.
Here is the distribution of R-factors for structures in PDB
deposited at similar resolution (in range between 1.75A and 1.85A):
Histogram of Rwork
for all model in PDB at resolution 1.75-1.85:
0.114 -
This is a perennial Q, and one without a good answer.
There are some pretty uncontriversible facts.
If you have atomic resolution your R and Rfree will be pretty close -
90-95% of data gives you a pretty well correct structure and the FreeR
will reflect that..
If you have low resolution and
( while I'm at it, freeR has nothing to do with model bias (which is
largely imaginary anyway, only a problem with low resolution molecular
replacement))
Phil
Phil, I understand what you're saying but 'model bias' in this context
has a wider meaning than just failing to rebuild the chain
If you have non-crystallographic symmetry the effects are uncertain,
but
in many cases this too gives you a lower than expected FreeR value,
and
again, that doesnt mean you have a better structure..
In general the difference in R and Rfree should be correlated with the
resolution, but there
Bias is defined as 'difference from expectation', so the isotropic
model
is almost certainly biased, as reflected in the higher-than-expected
Rwork Rfree.
Phil, sorry in my rush to go home I explained that badly: bias is
defined as 'difference between the expected and true values'. In this
You can also pick thin shells with SFCHECK
and with 12-fold NCS the referees will likely not be kind if you dont!!!
--
Mark
On 10/19/09 2:30 PM, Vellieux Frederic frederic.velli...@ibs.fr wrote:
One of these people (Bart Hazes
I think, correct me if I'm wrong) suggests to take reflections for the
R-free as thin shells in reciprocal space. The thin shell is omitted
completely from the target for refinement (I
But see Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):227-38. Epub
2006 Feb 22.
on why thin shells aren't necessarily the answer.
And note neither program mentioned, dataman nor sftools, will allow you to
extend the set
of shells to higher resolution if you want to follow the practice
To properly omit reflections from the Rfree calculations can be done
using reciprocal space masks as implemented in the program WEIGHTS from
the DEMON/ANGEL program suite (Vellieux, Hunt, Roy Read [1995], J.
Appl. Cryst. 28, 347-351). I don't have the time to do it. But people
are welcome to
The RFREE SHELL command in sftools is another way to select thin shells.
However, for the purist there is no clean way of getting rid of
correlations between the Rwork and Rfree sets that I know of.
To do it properly, the thickness of the thin shell should be larger than
the radius where the
Dear All:
I got a problem with a data set in R32 space group with a resolution of
2.6.
Pointless indicated that the space group was R32 and phenix triage showed that
there was a pseudotranslation in the ASU.
My protein is a hexamer and the matthew coeff. showed that there should just
On Monday 19 October 2009 12:43:43 Jerry McCully wrote:
Dear All:
I got a problem with a data set in R32 space group with a resolution
of 2.6.
Pointless indicated that the space group was R32 and phenix triage showed
that there was a pseudotranslation in the ASU.
My protein
Brad,
It looks like the chelator is a reducing agent added to media for
preservation, I guess.
The cure is not found yet. I'm just loading ~300 ml per one 5 ml
column and it so far serves me well.
The IEX approach did not work well. I've lost more than with IMAC after
3X dilution (with
Two very low-brow suggestions that might help:
1. Do a round of idealization in Refmac, to tighten up the geometry as
much as possible. Then return to your current approach.
2. Try using phenix.refine (with the same mtz, test reflections, latest
PDB, etc). The difference can sometimes be
On Oct 7, 2009, at 1:56 AM, Kevin Cowtan wrote:
William G. Scott wrote:
On Oct 6, 2009, at 1:32 AM, Morten Kjeldgaard wrote:
teleports the students across the hermeneutic circle ;-)
(As a consequence, I recommended the postmodernism generator
website to the students:
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