I believe you achieve completeness more quickly (fewer crystals) if you
just take random orientations. At least, that's what I learnt from Dave
Stuart.
phx
On 18/11/2011 04:20, Frank Murphy wrote:
Yanwu,
I surmise from your question that you are inquiring how to go about
collecting from m
I don't think one can generalise that much.
In the Stuart case of BTV, only 1-3 useful images per crystal could be obtained
if I remember correctly - so there the random strategy orientation makes sense.
I.e. if you collect one image and then wait until the orientation and strategy
is calculated
Hi Frank
I believe (at least part of) the key to the 30S ribosome structure was being
able to orient the crystals carefully and collect the data accordingly - see
Brodersen et al, Acta Cryst. (2003). D59, 2044-2050
Completeness, while important, ain't everything.
On 18 Nov 2011, at 08:26, Fra
Dear prospective PhD students,
for those considering coming to Spain, it may be worth applying for a La Caixa
fellowship.
The website is:
http://www.cnb.csic.es/content/about/lacaixa/index.php?l=0
You do not have to present a project, in fact you only choose which lab to go
to after being selec
Pointless will do the best it can with whatever data you give it, but if it is
already merged then it can only check for under-merging, or for reindexing
The normal use is for unmerged data as output by an integration program such as
Mosflm or XDS, as a prelude for scaling with Aimless or Scala.
Hi,
I apologize in advance as it is not a ccp4 related question, but over the
years, CCP4bb is synonymous with protein crystallographers virtual
university, at least for me.
Ok, now I do not have an easy access to crystallization robot, so I was
hoping if someone here have ever used the 96 well pl
Hi all,
I have data indexed in I23 with ~3000 unique reflections. Having set
aside 10% of these my refinements still go berserk. The maps do look
fine though. The same happens when reindexed in lower symmetries.
Phenix autobuild finishes for example with 28/40 and I get similiar
results (although
Hi,
I am routinely using the gryphon robot from Art Robbins.This instrument can
dispense 0.02microlitre at minimum. Your drops can dry out if you use such
low volumes you have to be really fast. You can set up 0.2 to 0.1 micro
litre drops using this for 96 well plates however the instrument needs t
Dear Crystallographers,
I am getting an error when I try to merge two mtz's from mosflm, one
with 180 and one with 360 frames, each from different but similar
crystals--see below. I can't imagine this really exceeds the max
number of records, so what am I doing wrong? Additionally but related,
wha
Depending on the crystal shape, "random orientation" is not always
random. Many crystals have tendencies of sitting themselves in one
predominant posture in the mount. Compounding this, many experimenters
have tendencies of rotating the mount into a specific orientation when
centering. Then crystal
Generally speaking, don't we agree that "planned" or "rational" is
better than "random?" (Having trouble understanding the argument for
randomness here...)
Jacob
On Fri, Nov 18, 2011 at 9:40 AM, Sanishvili, Ruslan wrote:
> Depending on the crystal shape, “random orientation” is not always random
There's a limit set in CCP4/lib/src/sorting_main.f
C NMAX_MEM increased from 1600 to 3200
PARAMETER (NMAX_MEM = 3200)
which you could change and recompile (:-))
You can combine unmerged files in Pointless, which is usually the best method,
but that reads everything into me
Okay, it seems there is utility to Pointless--problem solved! Maybe
developers should consider upping the limit, though?
Thanks very much,
Jacob
On Fri, Nov 18, 2011 at 9:45 AM, Phil Evans wrote:
> There's a limit set in CCP4/lib/src/sorting_main.f
>
> C NMAX_MEM increased from 1600 to
Pointless should supercede sortmtz, at least for most purposes, but I agree it
should be increased
Actually it's inconsistent in the source code, elsewhere there is
PARAMETER (NMAX_MEM = 1600)
but that may not matter
Phil
On 18 Nov 2011, at 15:50, Jacob Keller wrote:
> Okay, it see
sorry totally misunderstood your question, however if you can ship your
protein i can always try to setup a tray for you.
Shya
On Fri, Nov 18, 2011 at 9:34 AM, xaravich ivan wrote:
> Hi,
> I apologize in advance as it is not a ccp4 related question, but over the
> years, CCP4bb is synonymous with
Just enquiring on the off chance that someone has/knows of a teaching video
demonstrating the setting up of hanging and/or sitting drops for
crystallisation.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
On Fri, 2011-11-18 at 06:34 -0800, xaravich ivan wrote:
> Ok, now I do not have an easy access to crystallization robot, so I
> was hoping if someone here have ever used the 96 well plates for
> manually setting drops with much lower solution/sample volumes
> (0.1-0.2micro litres).
>
The best we
Hi Aaron,
here is what I would do:
- create 10-20 independent test sets containing 5% of reflections (make
sure lattice symmetry is taken into account - Phenix does it by default);
- solve and refine structure for each of the data set (make sure you use
such a refinement strategy so you don't get
Hi,
With the electronic Biohit 8 channel pipette you can set up 3x96 drops in 5
minutes. Lowest volume is 0.2 ul. We have used this system for a couple of
years with RNase free filter tips for RNA-protein complexes. With the recent
arrival of a shared Mosquito we have used the Biohit less but it
An excellent review of the specific damage reactions observed in
cryo-cooled MX is Burmeister (2000)
http://dx.doi.org/10.1107/S0907444999016261
There is also a "Beginner's Guide to Radiation Damage" that was
published in JSR a few years ago.
Burmeister's Fig 3 shows difference density appea
Hi,
I need to buy 24-well crystallization plates. I want to know the review of
crystallization plates other than Hampton research & Molecular Dimensions
(cheaper & still good to work with).
Has anyone used & liked the ones from Jena biosciences?
Thank you,
Poorva Dharkar
National Cancer Instit
Hello,
I wonder what everyone is using for sealing hanging drop slides on VDX
plates? For the most part, we paraffin oil but I am unhappy with it because
it is too think and too frequently there is break in the oil and the drop
dries too much. I find vacuum grease to be not terribly practical
Dow Corning Heavy Vacuum Grease, a 10 ml syringe and a shorter cut 200 µl tip
attached to the syringe.
Jürgen
On Nov 18, 2011, at 12:55 PM, Dima Klenchin wrote:
Hello,
I wonder what everyone is using for sealing hanging drop slides on VDX
plates? For the most part, we paraffin oil but I am unh
Vaseline (pure, with no additives) from CVS/Walgreens in a 10 ml syringe
and a pipette tip (wide bore) also works very well.
On 11/18/11 12:58 PM, Bosch, Juergen wrote:
Dow Corning Heavy Vacuum Grease, a 10 ml syringe and a shorter cut 200
µl tip attached to the syringe.
Jürgen
On Nov 18, 20
Hi Aaron,
You don't explain why you have so few reflections. Is it a small cell, low
resolution or just really bad data?
Assuming it's not the last one and your data is reasonably complete, I would
try this:
- Divide your reflections into six groups (and check that these
groups ar
I remember a technique that used warmed Vaseline (liquefied) in a shallow pan.
People would invert the plate and dip it into the liquefied Vaseline, then flip
it over to dry. I suppose one could use masking tape to cover the outer edge of
the plate to keep it Vaseline free. I am not sure how it
The is probably the cleanest and fastest way of greasing plates.
Take a 15ml Falcon tube and unscrew the cap. You will notice that the
cap is exactly the width as the well of the VDX plate. Using a fairly
wide bored metal syringe needle, pierce 8 holes into the cap from the
outside, along the
Haven't done this for a while, but what we used to do was mix Vaseline plus
mineral oil (both purchased for cheap at the local drugstore), and then apply
it using a 10 ml syringe with a pipet tip attached.
We used the mixture of Vaseline + mineral oil because Vaseline alone is too
viscous (unle
I have used melted Vaseline and a 10mL Erlenmeyer flask. The mouth of the
Erlenmeyer is the same size as the opening of the VDX plate. Dip flask mouth
in melted Vaseline, then press the mouth of the flask onto the opening of the
VDX plate.
- Original Message -
> From: "Dima Klenchin"
http://shane-anderson.com/ndxz-studio/config/clrodg.htm
Hello Ivan,
You can dispense 0.1-0.2 uL drops with the PB-100 repeating
dispenser from Hamilton and a 10 uL glass syringe. But it's rather
clumsy and hard on the hands. I don't recommend using it with 96 well
plates. It's too slow to do the whole plate at one time without your
drops drying up
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