Dear Marco,
I did not know autoxds, but google suggests that it is a csh(uarrrgh)-script
from SLAC. So as long as you have some c-Shell installed on your MAC, to script
should execute.
Maybe you can be more precise about what you mean by your last sentence to get
more accurate help.
Cheers, Tim
Dear Dave,
Here come my five pence...
I personally found stereo graphics useful in two cases.
1. When you first introduce students to biomolecular
structure and/or biocrystallography. Showing stereo
certainly helps 'building up' the initial fascination,
which is very important of course. But
I think you have been caught by a new REFMAC feature which tries to
design its own TLS groups including linked H2Os and ligands.
Check your tls output records and see what it has clustered into a group..
I am not sure how to disable this - at times I want to override any
automatic
On 03/03/2011 06:13 AM, Ting-Wei Jiang wrote:
Dear all experts,
I'm trying to calculate R-value (and free R) specifically which is between
data and the modified structure(refined by myself without help from any
program).I've looked the program for calculating a long while.Actually,I
found one
Dear All,
Please find below an announcement for a Scientic Programmer on the PROXIMA 2
beamline at Synchrotron SOLEIL. The position is a 2-year contract suitable for
a PXer with strong computing instrumentation skills or a Computing Engineer.
Dear all,
I got a reviewer comment that indicate the need to refine the structures at an
appropriate resolution (I/sigmaI of 3.0), and re-submit the revised coordinate
files to the PDB for validation.. In the manuscript I present some crystal
structures determined by molecular replacement using
No - and I dont think it is accepted practice now either..
I often use I/SigI 1.5 for refinement..
Look at your Rfactor plots from REFMAC - if they look reasonable at
higher resolution use the data
Eleanor
On 03/03/2011 11:29 AM, Roberto Battistutta wrote:
Dear all,
I got a reviewer
Roberto,
The reviewer's request is complete nonsense. The problem is how to best and
politely respond so as not to prevent the paper from being accepted. Best would
be to have educated editors who could simply tell you to ignore that request.
Since this issue comes up quite often still, I
Dear Roberto,
As indicated by others in reply to you the current best practice in
protein crystallography is not a rigid application of such a cut off
criterion. This is because there is such a diverse range of crystal
qualities. However in chemical crystallography where the data quality
from such
Dear Eleanor,
I don't think that was the case. I add tlsd waters exclude to a
refinement which as I understand it should prevent that. Also, I checked
the output files and the TLS groups only involve my protein, waters and
ligands aren't included anywhere. I can't explain why my TLS
On Thu, 2011-03-03 at 14:13 +0800, Ting-Wei Jiang wrote:
I'm trying to calculate R-value (and free R) specifically which is
between data and the modified structure(refined by myself without help
from any program).
At long last, someone escaped the tyranny and oppression of the
refinement
On Thu, 2011-03-03 at 12:29 +0100, Roberto Battistutta wrote:
Does anyone know the origin or the theoretical basis of this I/sigmaI
3.0 rule for an appropriate resolution?
There is none. Did editor ask you to follow this suggestion? I
wonder if there is anyone among the subscribers of this bb
On Wed, 2011-03-02 at 19:23 -0500, David Roberts wrote:
What I am really looking for is an answer to a
simple question in that is stereo a nice thing from a pedagogy
standpoint for showing students complex biomolecules.
Of course it is. Exactly how much excitement it generates among the
There seem to be quite a few rule followers out there regarding resolution
cutoffs. One that I have encountered several times is reviewers objecting to
high Rsym values (say 60-80% in the last shell), which may be even worse than
using some fixed value of I/sigI.
On 3/3/11 9:55 AM, Ed
On 02/28/2011 09:39 PM, Hena Dutta wrote:
I could not open the COOT GUI after installing either from
'coot-0.6.1-binary-Linux-x86_64-centos-5-gtk2.tar.gz' or from
'coot-0.6.2-pre-1-revision-3205-binary-Linux-x86_64-centos-5-gtk2.tar.gz'
I have managed to build a coot pre-release for
For myself, I decide on the high resolution cutoff by looking at the
Rsym vs resolution curve. The curve rises, and for all data sets I have
processed (so far) there is a break in the curve and the curve shoots
up. To near vertical. This inflexion point is where I decide to place
the high
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) I/sigmaI and not I/sigmaI.
A review of similar articles in the same journal will show what is typical
for the journal. I think you will find that the I/sigmaI cutoff varies.
This information can be used
My preferred criterion is the half-dataset correlation coefficient output by
Scala (an idea stolen from the EM guys): I tend to cut my data where this falls
to not less than 0.5.
The good thing about this is that it is independent of the vagaries of
I/sigma (or rather of the SD estimation) and
I think this suppression of high resolution shells via I/sigI cutoffs is
partially attributable to a conceptual misunderstanding of what these (darn)
R-values mean in refinement versus data merging.
In refinement, even a random atom structure follows the Wilson distribution,
and therefore, even
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
For myself, I decide on the high resolution cutoff by looking at the
Rsym vs resolution curve. The curve rises, and for all data sets I
have
processed (so far) there is a break in the curve and the curve shoots
up. To near
On Thu, 2011-03-03 at 08:08 -0700, Bart Hazes wrote:
I don't know what has caused this wave of high I/Sigma threshold use
but
here are some ideas
It may also be related to what I feel is recent revival of the
significance of the R-values in general. Lower resolution cutoffs in
this context
Does the position of this inflection point depend on the redundancy? Maybe it
does not; for high-redundancy data one would simply get a much higher
corresponding Rsym.
On 3/3/11 11:13 AM, Ed Pozharski epozh...@umaryland.edu wrote:
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
On Thu, 2011-03-03 at 09:34 -0600, Jim Pflugrath wrote:
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) I/sigmaI and not I/sigmaI.
A review of similar articles in the same journal will show what is
typical
for the journal. I think you will find
related to what I feel is recent revival of the significance of the R-values
because it's so handy to have one single number to judge a highly complex
nonlinear multivariate barely determined regularized problem! Just as easy as
running a gel!
Best BR
-Original Message-
From:
Hi,
I don't think XDS generates an Rpim value, does it? The XDS CORRECT
strep provides the old fashioned Rsym (R-FACTOR) plus R-meas and Rmrgd-F.
The curves look all the same though
Fred.
Ed Pozharski wrote:
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
For myself, I
Hi,
- phenix.fmodel will probably output it too or maybe there is some
phenix.get_me_my_damn_rfactor or such
as Eric pointed out earlier, the command
phenix.model_vs_data model.pdb data.mtz
will do exactly this.
Pavel.
P.S.:
phenix.fmodel is the tool to compute total model structure
Discussions of I/sigma(I) or less-than cutoffs have been going on for at least
35 years. For example, see Acta Cryst. (1975) B31, 1507-1509. I was taught by
my elders (mainly Lyle Jensen) that less-than cutoffs came into use when
diffractometers replaced film methods for small molecule work,
Well BR, do not underestimate complexity of running a gel! There are even more
harsh referees comments on gel appearance and quality
than comments on cutting data based on R,RF and sigmaI :-)
Especially when one is trying to penetrate into prestigious journals...
Dr Felix Frolow
Professor of
Dear Bernhard
I am wondering where I should cut my data off. Here is the statistics
from XDS processing.
Maia
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION NUMBER OF REFLECTIONS COMPLET R-FACTOR R-FACTOR COMPARED
I/SIGMA R-meas Rmrgd-F Anomal SigAno
I take the point about a tendency in those days to apply sigma cutoffs to get
lower R values, which were erroneously expected to indicate better structures.
I wonder how many of us remember this paper by Arnberg et al (1979) Acta Cryst
A35, 497-499, where it is shown for (small molecule)
I have to resend my statistics.
Maia Cherney wrote:
Dear Bernhard
I am wondering where I should cut my data off. Here is the statistics
from XDS processing.
Maia
On 11-03-03 04:29 AM, Roberto Battistutta wrote:
Dear all,
I got a reviewer comment that indicate the need to refine the
there are even more harsh referees comments on gel appearance and quality
than comments on cutting data based on R,RF and sigmaI :-) Especially when
one is trying to penetrate into prestigious journals...
Ok I repent. For improving gels there is the same excellent program, also
useful for
We should compile this discussion and send it as compulsive reading to journal
editors...;-)
Bert
On 3/3/11 12:07 PM, Simon Phillips s.e.v.phill...@leeds.ac.uk wrote:
I take the point about a tendency in those days to apply sigma cutoffs to get
lower R values, which were erroneously
When will we finally jettison Rsym/Rcryst/Rmerge?
1. Perhaps software developers should either not even calculate the
number, or hide it somewhere obscure, and of course replacing it with
a better R flavor?
2. Maybe reviewers should insist on other R's (Rpim etc) instead of Rmerge?
JPK
PS is
On Thursday, March 03, 2011 05:10:02 am Judith Reeks wrote:
Dear Eleanor,
I don't think that was the case. I add tlsd waters exclude to a
refinement which as I understand it should prevent that. Also, I checked
the output files and the TLS groups only involve my protein, waters and
First of all I would ask a XDS expert for that because I don't know exactly
what stats the XDS program reports (shame on me, ok) nor what the quality of
your error model is, or what you want to use the data for (I guess
refinement - see Eleanor's response for that, and use all data).
There is one
Original Message
Subject:Re: [ccp4bb] I/sigmaI of 3.0 rule
Date: Thu, 03 Mar 2011 10:43:23 -0700
From: Maia Cherney ch...@ualberta.ca
To: Oganesyan, Vaheh oganesy...@medimmune.com
References: 2ba9ce2f-c299-4ca9-a36a-99065d1b3...@unipd.it
just to clarify that, at least in my case, my impression is that the editor was
fair, I was referring only to the comment of one reviewer.
Roberto
Roberto Battistutta
Associate Professor
Department of Chemistry
University of Padua
via Marzolo 1, 35131 Padova - ITALY
tel. +39.049.8275265/67
I see, there is no consensus about my data. Some people say 2.4A, other
say all. Well, I chose 2.3 A. My rule was to be a little bit below Rmerg
100%. At 2.3A Rmerg was 98.7%
Actually, I have published my paper in JMB. Yes, reviewers did not like
that and even made me give Rrim and Rpim etc.
Dear All,
Relatively recent statistics on I/sigmaI and Rmerge in PDB deposits are
presented in two following publications:
1.Benefits of structural genomics for drug discovery research.
Grabowski M, Chruszcz M, Zimmerman MD, Kirillova O, Minor W.
Infect Disord Drug Targets. 2009 Nov;9(5):459-74.
Hello Maia,
Rmerge is obsolete, so the reviewers had a good point to make you publish Rmeas
instead. Rmeas should replace Rmerge in my opinion.
The data statistics you sent show a mulltiplicity of about 20! Did you check
your
data for radiation damage? That might explain why your Rmeas is so
The data statistics you sent show a mulltiplicity of about 20! Did you
check your data for radiation damage? That might explain why your Rmeas is
so utterly high while your I/sigI is still above 2 (You should not cut your
data but include more!)
So then I got that wrong - with that *high* a
Rmeas is always higher than Rmerge, so if my Rmerg is high I don't like
Rmeas either.
But that makes perfect sense now per Tim: the linear Rmerge gives for small
N (lower redundancy) always lower values and rises with redundancy to
approach Rmeas/rim for high redundancy.
I like the idea just
Dear all,
I am trying to optimize my crystal with additives. Since the yield of my
protein purification is very limited, I am wondering what is the most efficient
way to set up drops with additive to save my protein and not wasting additives?
I am setting up 1 to 1 drops with 0.2 ul
Hello CCP4BB,
We have a beautiful GE AKTA Explorer and an AKTA Prime available.
Please contact me directly at ress...@gmail.com or 510-344-6633 for
more info.
Thanks,
Erin
I don't like Rmeas either.
Given the Angst caused by actually useful redundancy, would it not be more
reasonable then to report Rpim which decreases with redundancy? Maybe Rpim
in an additional column would help to reduce the Angst?
BR
Maia
Tim Gruene wrote:
Hello Maia,
Rmerge is
higher redundancy lowers Rpim because it increases precision. However,
it need not increase accuracy if the observations are not drawn from the
true distribution. If pathologic behaviour of Rfactor statistics is
due to radiation damage, as I believe is often the case, we are
combining
Use robot. You only need 0.1ul*96=9.6ul of protein solution.
On Thu, Mar 3, 2011 at 7:59 PM, m zhang mzhang...@hotmail.com wrote:
Dear all,
I am trying to optimize my crystal with additives. Since the yield of my
protein purification is very limited, I am wondering what is the most
wondering if mosflm can automatically estimate the gain.
i.e. i gather it is still estimated the usual way.
-Bryan
Based on roughly 1500 complete Laue data sets
containing more than 45000 Laue patterns,
I can say the following:
How to collect Laue data?
1.) put crystal on (capillary or cryo is fine)
2.) switch on X-rays (or Neutrons)
for time-resolved studies select one or more pulses
else forget
Dear John,
of course you are right, apologies for my
little exaggeration.
Warmest regards
Marius
Dear Marius,
To these two centres to which you refer we can add:-
Diamond Light Source; contact person Prof David Allan (small molecule
Laue X-ray crystallography);
Institut Laue Langevin ;
Usually Mosflm will use a default value for the gain that depends on the
type of detector used. This value is not realistic for CCD detectors, that
is it is not really equal to the ratio of ADUs to incident X-ray photons,
however it satisfies typical images under the assumptions of pixel
not sure whether this option has been mentioned before ...
i think what we really would like to do is decide by the quality of the
density. i see that this is difficult.
so, short of that ... how about the figure of merit in refinement ?
wouldn't the fom reflect how useful our data really are ?
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