I dont want to comment much on the science behind FOM estimates - as
James points out after exptl phasing alone many reflections are
effectively unphased - if the FH/ FA for a reflection are very small
then you have no phase estimate at all, and if the F+ F- or FP FPH
measurements are weak any
In this lab there are as many takes on this as there are
crystallographers I think! It seems to depend on personality - are you a
wild optimist who traces connectivity at 0.5 Sigma - or a cautious soul
who hates to be wrong..
It seems to me that there are often disordered regions we can never
Eleanor Dodson wrote:
In this lab there are as many takes on this as there are
crystallographers I think! It seems to depend on personality - are you a
wild optimist who traces connectivity at 0.5 Sigma - or a cautious soul
who hates to be wrong..
Blimey, I think it's the other way round.
I agree this is very interesting -
The 'real' FOM is a great idea (we should start a campaign for real FOMs!)
What the 'real' FOM is trying to get at is the quality of the initial
experimental map. This could also be subsequently calculated for NCS-averaged
and density-modified maps
I am looking for published examples where hydrogen bond restraints
were helpful in refinement. Can anyone point me to some papers?
--
Bradley J. Hintze
Graduate Student
Duke University
School of Medicine
801-712-8799
Hi I installed ccp4-6.1.3 on an ubuntu 10.04 beta box.
It does not have bltwish and I was trying to install it using gcc 4.4.3 on a
64 bit ubuntu machine
The known patches for getting blt2.4z are already applied to the source ,
the documented problems on the ccp4i problems page are also as they
Dear Bradley,
a recent refinement of a protein complex at 4.3 A was stabilized by
using hydrogen bond restraints in secondary structures [1] (described in
the supplementary material). Subjectively, the additional restraints had
a small positive effect on the electron density interpretability
Dear All. A bit of publicity for a CCP4 workshop at the ACA. Garib Murshudov
and Paul Emsley are giving talks. Ronan Keegan, Stuart McNicholas and myself
will also be there giving overviews of the suite and CCP4MG (in it's new QT
guise)
Charles Ballard
CCP4
WK4: Getting the Most out of the
Dear Hari,
blt is, as far as I know, pretty deprecated and probably not updated anymore.
It also depends on tcl/tk version 8.4, not version 8.5 which is installed on
your system. Maybe you can try to downgrade and recompile.
Another, simpler way might be the following which works on the last 4
I have to say that I don't share James' enthusiasm for the FOM as a
useful statistic, even for experimental phases, and particularly not
in the SAD (and SIR) cases, which after all is what this thread is
supposed to be about. This is even without delving further into the
murky issues of wildly
Hi Tim,
Thanks a tonne Tim for the pointer on how bltwish is handled in debian.
A symlink from /usr/bin/wish to /usr/bin/bltwish.
Seems to at-least start ccp4i. Now to see if it will also plot my graphs
Hari
On Wed, Apr 14, 2010 at 10:23 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Dear
Katherine,
all good questions and all discussed previously on this very discussion
board. My personal opinion did not change much since 2007:
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19777.html
although I would probably amend couple of minor things. As for riding
hydrogens, take a
Hi all,
Sorry for a non-ccp4 query.
I will highly appreciate your comments on the expression:
I am trying to express HIS tagged ~60 kDa cytosolic protein from Bacillus in
E.coli pET expression system. I tried codon+ strain, time of expression
and various temperatures ( 18, 25, 30, 37C) for
On 09:41 Wed 14 Apr , Bradley Hintze wrote:
I am looking for published examples where hydrogen bond restraints
were helpful in refinement. Can anyone point me to some papers?
Try this one:
An improved hydrogen bond potential: Impact on medium resolution
protein structures. Felcy Fabiola,
Or Andrei's PhD thesis:
http://rna.ucsc.edu/~andrei/korostelev_disser.PDF
which as far as I recall contains some more technical details.
Pavel.
On 4/14/10 12:49 PM, Donnie Berkholz wrote:
On 09:41 Wed 14 Apr , Bradley Hintze wrote:
I am looking for published examples where hydrogen
Hi,
you did not mention if you just look for soluble expression.
However you could try an other fusion construct like MBP or GST-Tag to check
if the RNA do some strange things (secondary structures).
There are more strains available. For some unknown reason some strains work
some not.
I was surprised to get a few messages asking for our protocol for
reductive methylation of proteins for crystallization. We employ almost
exactly the protocol published by Walter et al, Structure, 2006. This is
a Ways and Means article that made us realize how easy it was to do
this regularly
Dear colleagues,
I would like to draw your attention to an upcoming educational webinar
that will cover data processing with d*TREK. This webinar is the 4th in
the previously posted webinar series to cover X-ray diffraction data
processing packages.
Next week's webinar, presented by Jim
Hi All
I had two crystals grown in same well, one is small and other is 10 times
bigger. I treated both crystal in same cryo and same time. The smaller one
diffracted to 2.5A and the bigger one to 6-7A. I was expecting the bigger one
to diffract high resolution.
I assume the bigger crystal
There are a couple of additional factors not taken into account here.
1. LN2 versus frozen in strem or propane etc
2. did you try to flash anneal the larger crystal
3. smeary diffraction from the big crystal or not ?
4. how much residual solvent was around your crystal when freezing ?
In general
50% solvent content in a small crystal is still 50% solvent content in
a large crystal given the same crystal form, so it's tough to use that
to explain loss of diffraction.
Very large crystals in my hands seem to suffer from more problems of
mechanical stress.
William
On Wed, Apr 14, 2010
I agree. Large crystals often diffract more poorly than smaller ones.
I would hazard a guess that large crystals may experience more
mechanical distortion during flash cooling, but it's just a guess. In
our lab, the sweet spot for most of our crystals is 0.3-0.4 mm. Larger
is usually worse, and
Like others have pointed out, I've often found very large crystals ( 0.4
mm) to not diffract as well, either due to growth defects or poor
cryoprotection. How large are the crystals you're talking about? You could
try chipping a piece off your large crystal and see how well that diffracts.
ho
Dear Crystallographers,
I am trying to determine the binding register of a helical peptide into a
binding groove of a protein of known structure. There are several known
peptide-protein complex structures of this protein in the PDB (each
containing the same protein but different peptides).
Dear Jurgen and Ho Leung
To add few more point regarding my question:
1. Crystal was first frozen in LN2 and then transfered to cryo stream (in
presence of LN2 in vial)
2. Anealing did not help (both short time and long time) - perhaps the crystal
dies.
3. Spots are clear to available
Yo Hari:
The symbolic link won't solve the problem.
I managed to scrape together a blt for tcltk 8.5 on OSX, so it is possible.
Most of the hacks in turn came from a different Linux distro (gentoo) so it
should be possible on ubuntu.
Here by the way is the patch:
1. look up Bacillus megaterium expression system (commercial, pretty
cheap relatively easy). It's easier to use than some of the
integration-based B. subtilis systems. Or you could ask around for a
suitable B.sut. shuttle vector as an alternative.
2. Bacillus codon set is heavily biased towards
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