Same here. I noticed this is very much dependent on which version of
the graphics driver you use. The very latest one (319.17) inverts the
stereo (which can sometimes be fixed by repeatedly switching between
mono and stereo). An older one (310.32) works fine (with a Quadro 600).
Andreas
Dear Colleagues,
If we may combine Ethan's quote from Stout and Jensen with Tim's meter:-
With film the estimating of a spot's blackness by eye is not a meter, it
originally was a person's eye aided by a reference strip of blackened graduated
spot exposures.
With measuring devices the
So, in SI units it would be a kilometerometer?
--dvd
On Wed, 19 Jun 2013, Edward A. Berry wrote:
an Odometer measures hod?s:
wikipedia: The word derives from the Greek words hod?s (path or gateway)
and m?tron (measure).
In countries where Imperial units or US customary units are used, it is
Hi Kay, hi all,
sorry for the -maybe- naive questions, but i'm struggling to get the GUI for
XDS going.
I'm on Mac OSX 10.8.4. The dmg installer and the script work nicely.
However, I have a couple of problems::
1.
I have placed the generate_XDS.INP script in the XDS directory
Dear All,
I have been working on a high resolution protein structure using Shelx
for refinement.
In the PDB output by Shelxl the hydrogen atom names are in duplicate
which is causing difficulty in PDB deposition.
I am aware of the use of shelxpro's B option to prepare for pdb
deposition, it
No, a kilometer is what they use in shooter video games.
On 20/06/2013 08:49, Gerard DVD Kleywegt wrote:
So, in SI units it would be a kilometerometer?
--dvd
On Wed, 19 Jun 2013, Edward A. Berry wrote:
an Odometer measures hod?s:
wikipedia: The word derives from the Greek words hod?s (path
As others say - the Rfactors look pretty good for MR, mine usually start
over 50% even with a better model and one hopes they then decrease..
But you say you took the Balbes model into phaser? and I think Balbes
automatically runs cycles of refinement so any comment on R factors may not
mean much.
hi Kay,
thanks a lot for the prompt reply.
Indeed the problem rises from the fact that the program is launched in a
non-bash environment, so one would have to add generate_XDS.INP to the PATH
of the Mac interface, rather than to the bash PATH.
I took the workaround of launching XDSgui from the
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Dear Swastik,
unless this is a structure from neutron data I recommend not to
deposit hydrogen atoms at all, because their positions are calculated
rather than refined.
Best,
Tim
On 06/20/2013 11:40 AM, Swastik Phulera wrote:
Dear All, I have been
Dear All,
I would like to bring to the ccp4b attention that a PostDoc position in
bio-physics is available in structural biology labs at Sanofi RD in Paris area.
Please see the announcement below.
Best regards,
Alexey
Alexey RAK, PhD
Structure-Design-Informatics / LGCR / Sanofi RD
13, Quai Jules
Dear Bulletin Board,
Prodded by pdb annotators, which are very hesitant to accept coordinate files
when their Rfactor does not correspond with our Rfactor, I had a look again
into some old data sets, which I suspect are twinned. Below are the results of
some twinning tests with the Detwin
Hi all,
I'd like to be able to automatically remove modeled/refined water molecules
that overlap regions of space that have been flagged as potential blobs
of interest in an initial difference density map.
My questions are:
1) Can I get Coot to output to a file the coordinates it spits out when
Dear Mitch (and Philip and Phil),
It is clear that I should give refmac a go with the non-detwinned F's and just
the TWIN command.
Thank you for your suggestions,
Herman
-Ursprüngliche Nachricht-
Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu]
Gesendet: Donnerstag, 20.
As a maybe better alternative, we should (once again) consider to refine
against intensities (and I guess George Sheldrick would agree here).
I have a simple question - what exactly, short of some sort of historic inertia
(or memory lapse), is the reason NOT to refine against intensities?
You are welcome. Let me also for the benefit of others who may
search the archives in the future, let me correct two errors
below - (typo and a miss-recollection).
Specially, I was thinking that phenix.refine was now able to refine
multiple twin laws, but according to Nat Echols on the phenix
Just trying to understand the basic issues here. How could refining directly
against intensities solve the fundamental problem of negative intensity values?
On Jun 20, 2013, at 11:34 AM, Bernhard Rupp hofkristall...@gmail.com wrote:
As a maybe better alternative, we should (once again)
If you are refining against F's you have to find some way to avoid
calculating the square root of a negative number. That is why people
have historically rejected negative I's and why Truncate and cTruncate
were invented.
When refining against I, the calculation of (Iobs - Icalc)^2
Yes higher R factors is the usual reason people don't like I-based
refinement!
Anyway, refining against Is doesn't solve the problem, it only postpones
it: you still need the Fs for maps! (though errors in Fs may be less
critical then).
-- Ian
On 20 June 2013 17:20, Dale Tronrud
Wouldnt be possible to take advantage of negative Is to extrapolate/estimate
the decay of scattering background (kind of Wilson plot of background
scattering) to flat out the background and push all the Is to positive values?
More of a question rather than a suggestion ...
D
From: CCP4
Seems to me that the negative Is should be dealt with early on, in the
integration step. Why exactly do integration programs report negative Is to
begin with?
On Jun 20, 2013, at 12:45 PM, Dom Bellini dom.bell...@diamond.ac.uk wrote:
Wouldnt be possible to take advantage of negative Is to
Sorry, perhaps what I was thinking was to use the Icalc to proportionally push
up the Iobs to push the negative Is to positive numbers.
But I guess that would bias the Iobs ?
Again just questions rather than suggestions.
D
-Original Message-
From: Douglas Theobald
The prior knowledge about Is is not merely that they are = 0, it's more
than that: we know they have an (approximate) Wilson distribution. AFAICS
incorporating that information at the integration stage would be almost
equivalent to the FW procedure. In fact it would probably not be as good
since
The integration programs report a negative intensity simply because that is the
observation.
Because of noise in the Xray background, in a large sample of intensity
estimates for reflections whose true intensity is very very small one will
inevitably get some measurements that are negative.
How can there be nothing wrong with something that is unphysical?
Intensities cannot be negative. How could you measure a negative number of
photons? You can only have a Gaussian distribution around I=0 if you are using
an incorrect, unphysical statistical model. As I understand it, the
I still don't see how you get a negative intensity from that. It seems you are
saying that in many cases of a low intensity reflection, the integrated spot
will be lower than the background. That is not equivalent to having a negative
measurement (as the measurement is actually positive, and
Intensity is subtraction: Inet=Iobs - Ibackground. Iobs and Ibackground can
not be negative. Inet CAN be negative if background is higher than Iobs.
We do not know how to model background scattering modulated my molecular
transform and mechanical motion of the molecule,
I recall we have
On Jun 20, 2013, at 1:47 PM, Felix Frolow mbfro...@post.tau.ac.il wrote:
Intensity is subtraction: Inet=Iobs - Ibackground. Iobs and Ibackground can
not be negative. Inet CAN be negative if background is higher than Iobs.
Just to reiterate, we know that the true value of Inet cannot be
HiPlease can I ask about how can I put NAG to asparagine in coot (I think its 2NAG that I can put in density) and if possible to refine itin refmacthen.Thanks in advance for help RegardsMonikaMonika PathakUniversity of NottinghamNG7 2RD
This message and any attachment are intended solely for the
Douglas, I think you are missing the point that estimation of the
parameters of the proper Bayesian statistical model (i.e. the Wilson prior)
in order to perform the integration in the manner you are suggesting
requires knowledge of the already integrated intensities! I suppose we
could iterate,
Douglas,
the intensity is negative if the integrated spot has a lower intensity than the
estimate of the background under the spot. So yes, we are not _measuring_
negative intensities, rather we are estimating intensities, and that estimate
may turn out to be negative. In a later step we try
Dear all,
I just observed a puzzling phenomenon when purifying a refolded protein with
size exclusion chromatography. The protein was solubilized by 8M Urea and
refolded by dialysis against 500mM Arginine in PBS. The protein is 40KDal and
is expected to be a trimer. The puzzling part is the
Kay, I understand the French-Wilson way of currently doing things, as you
outline below. My point is that it is not optimal --- we could do things
better --- since even French-Wilson accepts the idea of negative intensity
measurements. I am trying to disabuse the (very stubborn) view that
Douglas,
as soon as you come up with an algorithm that gives accurate, unbiased
intensity estimates together with their standard deviations, everybody
will be happy. But I'm not aware of progress in this question (Poisson
signal with background) in the last decades - I'd be glad to be proven
If your protein elutes very late, that means it's binding to the column matrix
(so all estimates of size go into the trash). Check to see that the ionic
strength of buffer is reasonable (equivalent to, say, 150 mM NaCl). If so, then
the only solution is to go to a different matrix type.
Pat
On
Well, I tend to think Ian is probably right, that doing things the proper way
(vs French-Wilson) will not make much of a difference in the end.
Nevertheless, I don't think refining against the (possibly negative)
intensities is a good solution to dealing with negative intensities --- that
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Dear Douglas,
why don't you try this and publish the results? As Kay already pointed
out everybody would be delighted if we can get better data - if
including negative intensities leads to better models, I think most
crystallographers could not be
Hi Zhen,
I'm not sure that binding to a monoclonal antibody is good evidence that the
protein is in a natively folded state. I would be suspicious of such a result
as the protein could be improperly, which is causing it to interact with the
column matrix. It could be useful to use some other
Measurement worth not very much if simultaneously error of measurement is not
considered.
10 counts intensity on the top of 1 counts background is close to nothing.
10 counts on the top of 1 count background is an excellent intensity.
Simultaneously with diffraction several types of X-ray
On 20 June 2013 20:46, Douglas Theobald dtheob...@brandeis.edu wrote:
Well, I tend to think Ian is probably right, that doing things the
proper way (vs French-Wilson) will not make much of a difference in the
end.
Nevertheless, I don't think refining against the (possibly negative)
Hi Kushol,
No. The void for the column is 8ml and the whole volume of the column is 24ml.
You must be talking about a different column.
Zhen
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kushol
Gupta
Sent: Thursday, June 20, 2013 4:09 PM
To:
Mea culpa - I'm thinking minutes at 0.5 ml/min, not mLs!
(clearly I'm overdue for my afternoon caffeine...)
Kushol
-Original Message-
From: Zhang, Zhen [mailto:zhen_zh...@dfci.harvard.edu]
Sent: Thursday, June 20, 2013 4:18 PM
To: 'Kushol Gupta'; CCP4BB@JISCMAIL.AC.UK
Subject: RE:
Hi Zhen -
Superdex is known to have some ion-exchange characteristics, so that it
can weakly interact with some proteins. This is why the manufacturer
recommends including a certain amount of salt in the running buffer. I
have had the same experience with a few proteins, including one that
Hi,
The intensity-based likelihood refinement target was in our paper in 1996
(http://www-structmed.cimr.cam.ac.uk/Personal/randy/pubs/li0224r.pdf). It's
perfectly happy with negative net intensities. Basically, the question you're
asking with a negative net intensity is what is the
Hi Matthew,
Thanks a lot. That is a great idea. I will try the high salt and worry about
the crystallization later.
Zhen
-Original Message-
From: Matthew Franklin [mailto:mfrank...@nysbc.org]
Sent: Thursday, June 20, 2013 4:34 PM
To: Zhang, Zhen
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re:
Yes, the function implemented in CNS includes the sigma term.
Best wishes,
Randy
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills
I am posting this job opening for a beamline Scientist position on behalf
of Prof. D D Sarma. Interested candidates may write to him directly. The
advertisement reads as below:
*Beam-line Scientist and Engineer Positions*
*at Elettra, Italian Synchrotron source, Trieste, ITALY*
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