> Sure, no while lines considered in the edge calc, for example.
That and (more important) that
2*abs(a-b)/(a+b) > 2*abs(sqrt(a)-sqrt(b))/(sqrt(a)+sqrt(b))
See Acta Cryst. D61, 1437–1448.
(btw, while is overrated, use for and a break statement)
p
I think you need to first address the issue of radiation damage.
Radiation damage can prevent you from solving the structure even
before it affects Rsym or I/sigma.
I haven't merged data from multiple crystals to solve a MAD structure,
but I'd try it in your case, with inverse beam data collection
On Mar 19, 2009, at 3:26 AM, Andrew Purkiss-Trew wrote:
On Wed, 2009-03-18 at 18:19 +, Frank von Delft wrote:
Maybe, but images without experimental context (sequence? ligands?
purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!!
relationship to the other 15 similar datasets)
Rafal,
Actually, things only really started to change last month...
Please see http://pymol.org and scroll down most of the way to the
February 13th entry regarding the $600 Zalman ZM-M220W stereo-capable
LCD.
In my opinion, that is the best option on the market until the "powers
that be" star
<|delta F|>/ *c \approx < |delta I|/ I > ,
with c somewhere between 2.5 and 3.
Bijvoet amplitude ratios seem always more pessimistic then they should be.
The 4 to 5% <|delta F|>/ would translate into a 10 to 12% expected
difference for individual intensities.
P
2009/3/20 Bernhard Rupp :
> Wha
> Bijvoet amplitude ratios seem always more pessimistic then they should be.
Sure, no while lines considered in the edge calc, for example.
BR
Just to dot the T's and cross the I's here - I actually don't want to *have
to* deposit images routinely. I definitely hope that this is not going to be
a mandatory step in PDB deposition any time soon - for a simple reason: at
the moment this is too much trouble. Connections are too slow, and imag
And by then, the IUCR will have established the CFDU (Crystallographic Fraud
Detection Unit), onto which Jack Bauer would be enlisted as a consultant ("24"
may still be running, who knows, so Jack won't be able to serve full-time on
the job). This would be fun.
Boaz
- Origina
It took from the 'official' IUCR recommendation in 2000
Guss M (2000) Guidelines for the deposition and release of macromolecular
coordinate and experimental data. Acta Crystallogr. D56(1), 2.
until Feb 2008 for structure factor amplitude deposition to the PDB
to become mandatory.
Nature start
What is not true?
Also in your case the applet estimates an expected
4-5% signal which is quite doable with decent data.
BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tommi
Kajander
Sent: Friday, March 20, 2009 3:43 PM
To: CCP4BB@JISCMAIL.AC
Dear CCP4BB users,
After one long year I'm back to crystallography again :) Actually I try to
organize a crystallographic lab in new work place. Of course one of
important thing what I need is a good computer machine for
crystallographic calculations and molecular graphics. And now I need yours
ad
Bernhard Rupp wrote:
I only scratched the surface and I think it would be hard work to fake
the images in a way that later expert forensics would
not readily provide evidence. Also, there are 'watermarks' available from
cryptographic methods that are even 'post-processing' resistant.
A practi
Kumar,
As many here have pointed out - this is not likely to work. However if you
already have crystals, why not to try phasing using tried and true heavy
atom derivatives. Who knows, you might get lucky and one of them might
actually improve the diffraction (this happens more often than people
this cant be true,
in the idea case (not Rmerge 15%, then again one can apply a resolution
cutoff, perhaps, while this sounds like a very desperate case) the
answer must be yes. didnt do the calculation right now (but it
_should_ back this up)
we for instance have solved a structure long time a
You can try using affinity tags on both the N- and C-termini of the
protein, eg. MBP on N and His on C.
ho
> Date: Thu, 19 Mar 2009 23:53:14 +
> From: Kn Ly
> Subject: purification
>
> Hello everyone,
>
> I am expressing a 100 KDa eukaryotic membrane protein in E coli. The prot=
> ein
One can estimate this from
http://www.ruppweb.org/new_comp/anomalous_scattering.htm
and the answer as Jim says is no.
BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jim
Pflugrath
Sent: Friday, March 20, 2009 1:08 PM
To: CCP4BB@JISCMAIL.AC.UK
S
Well, what do you expect the anomalous signal contributed from your 45
seleniums in a perfect world to be when the asymmetric unit contains 1300
aa? Do you think a dataset with Rmerge of ~15% is good enough to detect a
signal of even 2%? (Note: I did not do the calculation, so I just made up
Radiation Damage? Why don't you try scaling back on the time of each frame, get
better completeness and redundancy, while taking a hit on resolution? That
could get you your heavy atoms, and then you could apply those phases to a
"roasted" crystal. The heavy atoms are the first to go, it seems.
Hello CCP4bb members,
I have been trying to obtain phases for a protein which contain ~1300aa. We
have obtained native data to a resolution of 3.3A (Space group I222 or
I212121). But we are having tough time phasing it.
'Se' labeled crystals diffracts maximally up to 3.5 to 4 A and dies very
quic
Thomas,
The Areaimol program within the CCP4 suite should do what you're looking
for: http://www.ccp4.ac.uk/html/areaimol.html Although its a calculation of
surface accessability, you can delete sections of your protein to get at the
buried area between two sections of your protein.
Cheers, Jim
Hello all
can any one suggest any server or tool which can calculate the burried
surface area between the domains of the same monomer? PISA calculates the
interfacial surace area between the monomer or oligomer. Can areamol
calculate it?
Thanks in advance
Thomas
I just want to emphasize the usefulness of MLFSOM as a educational
tool. I made numerous figures showing principles and problems of
data collection using James' program. I can also assure you that in
order to use it properly, you need to know something about image data.
I only scratched the surfa
Hi Kien,
As Artem pointed out earlier. Are you sure that your protein folded
correctly. You want to make sure that the protein is expressed in lipid
membrane not in inclusion body. If so, considering changing the host might
be a good idea.
Also, did you use any kind of detergent when you extract
Steganographic encoding of a PGP-encoded graphical segment should not be
difficult to incorporate...
The problem of course is that the delicate signal of such a 'hidden'
message would be subject to deliberate erasure unless the encoding is
actually done on the level of reflections themselves (i.e.
Hi all,
I am using refmac in ccp4i 6.1.1 (installed in windows). It runs well when
using automatic weight, but failed when using user-specified weight (0.12 in
this case). I attach the error message as follow. Your help is very much
appreciated.
..
18 0.2064 0.2348 0.8464076
After consultation with Ton Spek, I should correct my last email.
It turns out that my 'watermark' was not clever enough, because
PLATON - his program used to make the picture that I had randomly
picked as an example - can emulate the XP watermark (the way of
shading the ellipsoids which I intende
Dear Kien,
you might also try a different resin/ metal ion. If I remember correctly,
the technician where I did my PhD had much better results with a Talon
resin using Co instead of Ni: you can use much less Imidazole, only 5-10mM
for washing and 50mM for elution.
If you can go back to cloni
Try running the Ni column as fast as possible and putting
concentrated EDTA in the fraction collector tubes before you
start, to minimize opportunities for metal-dependent proteases.
It may not be a magic bullet but it can't hurt.
Phoebe
Original message
>Date: Thu, 19 Mar 2009 23:53:1
Felix
I would be very surprised if anyone could calculate the expected Rfree
in this case with any degree of reliability, since it seems to have been
refined with a combination of TLS and rigid-bond/sphericity anisotropic
ADP restraints. Taking account of restraints, particularly thermal ones
whi
I must add something...
ID14-2 beam line in our hands produced during first decade of 2000's
data sets that
for structures at about 1.8 - 1.6 Angstrom constantly leaded to a very
good R - Rfree (in the range of 12 %-18%)
As an example see PDB entry 1Y9A. If will be needed I will supply
diff
Hi Kien-
Are you basing extensive proteolysis (degradation) on an SDS-PAGE result
alone? Are you monitoring the elution profile from Ni/NTA? Do you see
numerous A280 peaks for your elution? Sample prep of membrane proteins for
SDS-PAGE is very trial-and-error. Heating the samples may cause weird
ag
Dear James,
About 30 years ago I wrote a clone of the program ORTEP; the clone
was called XP, but unfortunately Microsoft later stole the name
and brought it into disrepute. So that I would always be able to
see at a glance which plots were 'genuine ORTEP' and which were
my clone, I built in a s
Hi James
I think the answer to your question about the 'R-factor gap' is easy to
answer (but not so easy to solve!). It's obviously due to the
inadequacy of our models, particularly with regards to thermal motion
(anisotropy, anharmonicity etc), disorder & motion correlation/diffuse
scatter, also
Yes, Harry, indeed there is a program for simulating diffraction
patterns. You can get a development snapshot of it here:
http://bl831.als.lbl.gov/~jamesh/mlfsom/development_snapshot.tar.gz
MLFSOM (mosflm in reverse) is not the only program of its kind in
existence and I don't think it is a go
Sigma-Aldrich has such tool under the advanced search option.
Anthony
On Fri, 20 Mar 2009 09:13:38 +0100, cedric bauvois wrote
> Dear All,
>
> Sorry for the off-topic question.
>
> Is there an easy way to search "chemically close" molecules and know if they
> are commercially available ?
>
> Ma
Dear All,
Sorry for this off-topic question.
I am looking for the coordinates of the full (not only the
carbohydrate part) Gb3 (Globotriaosylceramide) and GM1 glycolipids.
I am pretty sure that the Gb3 glycolipid has been solved by NMR
(Nunez, 1982).
Any help by providing me the coordinat
Dear All,
Sorry for the off-topic question.
Is there an easy way to search "chemically close" molecules and know if they
are commercially available ?
Many Thanks.
--
..
Dr. Cedric Bauvois
Cristallographie des protéines
Institut de
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