Dear Bryan,
The quick answer is no. As David Waterman
mentioned, it has a default value for the gain for each type of
detector that it can deal with.
A more detailed answer. An incorrect value for the gain can be
indicated by values of the BGRATIO which differ signific
Dear All,
spotted a mistake in my response, please see the correction below (in
bold):
There are a host of caveats in this procedure. For example, if the
images contains significant diffuse scatter around the Bragg spots,
the BGRATIO may be above 1.0 ... this is probably the commonest
e
Maia,
provided radiation damage is not a major detrimental factor, your data
are just fine, and useful also in the high resolution shell (which still
has of 2.84 so you could probably process a bit beyond 2.25A).
There is nothing wrong with R_meas of 147.1% since, as others have said,
R_mea
Dear Roberto,
Overnight I recall an additional point:-
In chemical crystallography, where standard uncertainties are
routinely avaliable for the molecular model from the full matrix
inversion in the model refinement, it is of course possible to keep
extending your resolution until your bond distanc
Hi,
Could anyone recommend a reasonably priced (i.e. less than £3000) cooled
incubator for crystallisation plates? We plan to initially use this at 4C but
flexibility would be useful.
One that we have considered is the LEEC LT2J
http://www.appletonwoods.co.uk/acatalog/LEEC_Cooled_Incubator.htm
Applications are invited for 3 year PhD studentships in my lab, available for
October 2011 in the Department of Biological Sciences at the University of
Essex, Colchester.
The studentship titles are:
"Defining the structural factors that control ligand discrimination in
haemoproteins"
"Using X
Dear all,
just to say that I really appreciate and thank the many people who spent time
responding to my issue. I have read with much interest (and sometimes with fun)
all comments and suggestions, very interesting and useful.
Thanks a lot,
Bye,
Roberto.
Roberto Battistutta
Associate Professor
This is very closely related to the way in which I would like to think about
this: if you consider adding another thin shell of data, are you adding any
significant information? Unfortunately as Garib Murshudov has pointed out, we
don't have any reliable way of estimating the information content
hi
Recently on a paper I submitted, it was the editor of the journal who wanted
exactly the same thing. I never argued with the editor about this (should have
maybe), but it could be one cause of the epidemic that Bart Hazes saw
best regards
Marjolein
On Mar 3, 2011, at 12:29 PM, Roberto
On Fri, 2011-03-04 at 10:39 +, Hough, Michael A wrote:
> Could anyone recommend a reasonably priced (i.e. less than £3000)
> cooled incubator for crystallisation plates?
Consider wine coolers - many thermoelectric (vibration-free) models are
available. Normally they don't go down to 4 degrees
Kay,
Thank you for your explanation. The radiation damage was not the factor,
but there was something strange about this crystal (actually two
crystals had the same strange behavior). I could not process them in
HKL2000, but it showed the problem (see pictures in the attachment). The
processi
Hi CCP4ers,
Is there any place from where I could download .pdb files of LPS lipid A
from different bactiria?
Thanks a lot in advanced.
regards,
Ariel
Hi James,
I remember that P1 did not help. That was like 2 years ago. That crystal
was very important at that time, so I had to use it. There were many
other crystals since then (native, mutants and complexes) in the same
space group without problems. But also I had even a more weird crystal
Hello all,
I've been converting my XDS files (XDS_ASCII.hkl) to mtz using pointless and
then running scala to get the work mtz. I like this procedure because I get
useful info, (such as Rpim), that I don't know how to get otherwise. I there
any advantage/disadvantage of using this procedure inst
Dear Community,
In trying to trouble shoot an experiment I have become interested in
the cellular process that regulates the insertion and proper
orientation of membrane proteins. I am looking for references for how
a GPCR is correctly oriented during expression (i.e. the extra
cellular d
Hi Justin,
I'm not sure if there are papers regarding this for GPCRs, but the phenomenon
you're referring to is the "positive inside rule". This basically means that
the SecY translocon (in a way that is only partially clear) mediates membrane
protein insertion in such a way that the (net) posi
Hi Justin,
Since GPCRs are polytopic a-helical transmembrane proteins, it is very
likely that (1) insertion into the membrane is primarily performed by the
Sec61 complex AKA translocon and (2) targeting to the membrane would be
controlled by the signal recongition particle and its receptor. the la
In addition to Bert remarks, you can read this paper from the positive
inside rule instigators.
Seppälä S, Slusky JS, Lloris-Garcerá P, Rapp M, von Heijne G. Control of
membrane protein topology by a single C-terminal residue. Science. 2010
Jun 25;328(5986):1698-700. Epub 2010 May 27. PubMed P
Begin forwarded message:
From: Graeme Winter
Date: March 4, 2011 4/3/11 - 4:51
To: José Trincão
Subject: Re: [ccp4bb] XSCALE vs scala
Hi Jose,
if you are following the usual XDS procedure, the data will have already been
scaled by the XDS CORRECT step. XSCALE will perform essentially the sa
Am 04.03.2011 11:11, schrieb Kay Diederichs:
There is nothing wrong with R_meas of 147.1% since, as others have said,
R_meas is not limited to 59% (or similar) as a refinement R-factor is.
Rather, R_meas is computed from a formula that has a denominator which
in the asymptotic limit (noise) appr
Dear All,
I have two questions:
1) I have collected multiple, native datasets (5) from the same
crystal (different parts of the crystals exposed with different
transmission and oscillation angles). Each dataset on its own is close
to complete (96-98 %). Naturally, differences in exposure,
I have found that the best way to get the GAIN "right" in MOSFLM is to
have a look at the optimum "Sdfac" parameter at the end of SCALA (the
first of the three SDCORRection values). Specifically, if SDFac is > 1,
then you need to increase the GAIN. This is because SDFac>1 means that
the spots
Dear Phil,
I completely agree with you, your words seem to me the best
"philosophical" outcome of the discussion and indicate the right
perspective to tackle this topic. In particular you write "In the end, the
important question as ever is "does the experimental data support the
conclusions drawn
Dear ccp4bb
On behalf of Professor Geir Christensen I would like to draw your attention to
a post position in molecular biology
http://uio.easycruit.com/vacancy/519990/70331?iso=no
Please contact Geir Christensen for further information
J. Preben Morth, Ph.D
Group Leader
Membrane Transport Gro
Hi guys:
I know this has been asked before, but I want to get (current) opinions and
observations once again. Every once in a while, you work with a protein that
needs to have a little something added to the buffer to keep it soluble. The
most common trick is addition of glycerol (usually 5-10%)
Hi Tom,
Adding glycerol to (crystallization) buffers is a very common practice when
working with membrane proteins. Many membrane proteins have been crystallized
(perhaps even the majority) with glycerol, even up to 30% v/v. So, at least for
membrane proteins, there is no problem.
Bert
On 3/
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