lei feng wrote:
I am wondering , do we need uninstall the previous version of coot to
install this?
No. Many group use more than one version of Coot.
Ah, but perhaps you mean WinCoot? My (limited) experience is that you
can install right over the top of the old one.
Paul.
I am wondering , do we need uninstall the previous version of coot to
install this?
No. Many group use more than one version of Coot.
Ah, but perhaps you mean WinCoot? My (limited) experience is that you
can install right over the top of the old one.
WinCoot can be installed on top of
The other way round.
High solvent==low resolution
Low solvent==high resolution
Since the resolution limit depends on subjective criteria (source,
dose, I/sigI limit) in our test we always had a better correlation
between Wilson B (rather than resolution) and solvent content.
A.
Sent from
how about this for a general idea:
resolution is related to order in the crystals, more order =
diffraction to higher resolution
the order is determined by crystal contacts, stronger crystal contacts
= more order
more solvent means, on average, less close packing and less crystal
contacts
Dear all,
We are pleased to announce the
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*The routine accessibility, on some macromolecular crystallography (MX)
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mjvanraaij wrote:
how about this for a general idea:
resolution is related to order in the crystals, more order = diffraction
to higher resolution
the order is determined by crystal contacts, stronger crystal contacts =
more order
more solvent means, on average, less close packing and less
Ah. Found the paper: Kantardjieff Rupp (2003) Prot. Sci. 12, 1865.
Matthews coefficient probabilities: Improved estimates for unit cell
contents of proteins, DNA, and protein-nucleic acid complex crystals.
There is a nice figure showing that data from the PDB shows a clear
correlation between
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Deal All:
I have a 2.0 A data for a SeMet protein (native crystal not available
yet!) that has 6 Se sites.
The cell comes out to be 65 67 101 and the angles are all very close to
90. The data set was collected in house with Cu 1.5418 A
We integrated and scale in orthorhombic and the
Dear Subbu,
One more thing you can do is to search with an ensemble of structures (4
in your case) for molecular replacement.
Fred.
Narayanan Ramasubbu wrote:
Deal All:
I have a 2.0 A data for a SeMet protein (native crystal not available
yet!) that has 6 Se sites.
The cell comes out to be
In my experience, even when rather magically Phaser works with 20-25% identity,
with 2.0 data you cannot always proceed to change and refine your structure.
I would focus on the Se synchrtron data, or collect a very redundant set at the
home source, which should allow you to find the Se and do
Perhaps more tantalizing:
http://www.engadget.com/2009/10/22/sonys-360-degree-3d-prototype-displays-blown-minds-video/
There's a YouTube of it too:
http://www.youtube.com/watch?v=lAS55_RngoQ
If a higher resolution version could be made it might be of interest to our
community. It sounds
I assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit? Otherwise,
how would one author alone perpetrate this kind of thing? He pretends to go
to the synchrotron, comes back with the hkl file, and goes from
He pretends to go to the synchrotron, comes back
Thats what I do all the time. Instead, I go to lane splitters /
jupiter for pizza and beer.
P
On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu
wrote:
I assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit? Otherwise,
how would one author alone perpetrate this kind of thing? He
This kind of unfortunate situation only reinforces
the notion that there must be some sort of laboratory
oversight/communication/mentoring/documentation procedures in place. In
my research lab (populated by a postdoc and a bunch of undergraduates)
raw images and data processing log files are
Some of you might be curious about the Ajees et al debacle that Jacob
mentioned in his message. Here are two links:
Nature Brief Communication that questioned the validity of one of Murthy's
structures:
http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html
Murthy's rebuttal:
Tanner, John J. wrote:
Some of you might be curious about the Ajees et al debacle that Jacob
mentioned in his message. Here are two links:
Nature Brief Communication that questioned the validity of one of Murthy's
structures:
After a thorough examination of the available data, which included a
re-analysis of each structure alleged to have been fabricated, the
committee
found a preponderance of evidence that structures 1BEF, 1CMW,
1DF9/2QID,
1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely
than
If that's of any consolation for us crystallographers, this situations arise
in other fields too. Here is another example. See this link:
http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html
Boaz
- Original Message -
From: Roger
It seems that at least some of the primary authors, were starting PhD students.
For Ajees, as far as i know, he was given the mtz as soon as he joined the lab,
told that they have this data for a while, and asked to see
if the new software would do it. Not difficult to imagine.
A.
==
I assume
Matthew Franklin wrote:
Once again, I'd like to get the community's thoughts: should we ask the PDB to
stop using 0 and 1 in its IDs?
I'll get off the soapbox now.
I would be all for it... Having tried to downloade 1o08 and gotten it
screwed up Especially when journals use a
Thanks for bringing this article to our attention. I went ahead and created
a table of the PDBs in question including links to the structures, journals
and citations. My hope is that it will save others time trying to track
down this information.
http://bit.ly/5KqaRF
Hope it helps.
Sean
Actually, I don't think that should be any consolation at all... As
scientists, from whatever field, we should be appalled by this kind of
mischief from anyone that calls themselves scientists. Not only it has
effects on further research, delaying science sometimes by years, but it
just gives an
I wish to point out (as I unsuccessfully did to Nature) that
by just READING the infamous Table 1 (data collection and refinement stats,
hidden in the supplemental material) any review worth its name should
immediately have raised multiple red flags. Check for yourself.
Also the B-factor
For previous debate on this issue see (in CCP4 archives)
https://www.jiscmail.ac.uk/cgi-bin/webadmin?S2=CCP4BBq=s=The+importanc
e+of+USING+our+validation+toolsf=a=b=
I think Eleanor started it
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708L=CCP4BBP=R75676
And of course it is deja vu
Hi,
If I were you, I would collect a redundant dataset (~15-20 or even higher if
possible) at home and use the anomalous flag in Scalepack/Denzo. You should
be able to pick up the anomalous differences (especially with data to 2.0A)
for Se, even at CuKa wavelength at home!
Good luck!
Se.png
Hi everyone-
I was searching for some information on what might be the best way to
add N-linked sugars in coot, and Google has let me down. Searching
adding sugars in coot returns a very nice recipe for Coot Pudding.
Recipe for Coot Pudding - American Coots
http://www.beakycoot.com/pudding.html
Dear ccp4bb'ers,
I draw your attention to this information. Please spread the news.
Thank you in advance
**International Workshop Macromolecular Cristalography :
Introduction and Applications**
**April 26 - May 7, 2010* *
*Institut Pasteur de Montevideo*
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