I find that the superposition in CCP4MG is the most flexible and easy to
use implementation of any program I've used. There are multiple
superposition methods each with the ability to select residues or atoms.
It's very powerful.
CCP4MG also happens to produce very pretty pictures!
Isaac
On 5 Feb
In addition to the previous suggestions, if you have a metal-binding
protein, beware of acidic compounds chelating the metal and stripping it
out of the protein, as this often lead to the effect you observed as well.
Isaac
On 5 Feb 2015 13:45, Monica Mittal monica.mitta...@gmail.com wrote:
Hi
Dear CCP4BB users,
For additional information on this matter, please see:
wwPDB Statement on Retraction of PDB Entries
http://www.wwpdb.org/documentation/UAB.php
and
Safeguarding the integrity of protein archive
/Nature/ (2010) *463*:425. doi:10.1038/463425c
On Friday, 06 February, 2015 13:38:14 Rachel Kramer Green wrote:
Dear CCP4BB users,
For additional information on this matter, please see:
wwPDB Statement on Retraction of PDB Entries
http://www.wwpdb.org/documentation/UAB.php
and
Safeguarding the integrity of protein archive
Fred,
as you know discontinuous lattice is not physically possible. Therefore first
make sure to exclude your and deposition errors like a wrong space group and
cell constants. However, it may be that some molecules are disordered and
therefore absent in the structure solution. If there are
Haven'tthat paper and the associated structure been retracted?
http://www.nature.com/news/2009/091222/full/462970a.html
There was a huge scandal when it was discovered that Krishna Murthy had
falsified data, including the structure you refer to.
See
Actually, if you go back through the archive of CCP4-BB from the first time
this came up, I think you'll find that there are real crystals with apparent
gaps in the packing. This can arise because of statistical disorder, where
there are two or more ways that a statistically-disordered layer
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Smith,
The sca file most likely does not contain flags. pointless can read
the sca file, standardise it to ccp4 standards and freerflag marks
random reflections. You should use the maximum of 500 unique
reflections or 5% of the unique
Not in real crystal structures ;)
Cheers,
Robbie
Sent with my Windows Phone
Van: Kerff Fredmailto:fke...@ulg.ac.be
Verzonden: 6-2-2015 12:02
Aan: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] Absence of contact between layers in a
why are these structures still in the PDB?
On 6 Feb 2015, at 11:08, David Briggs drdavidcbri...@gmail.com wrote:
Haven'tthat paper and the associated structure been retracted?
http://www.nature.com/news/2009/091222/full/462970a.html
There was a huge scandal when it was discovered that
Unfortunately, the structure and associated paper for PDB id 2hr0 has _not_
been retracted, or marked as invalid.
The University of Alabama had a note about it, but only some of the
affected PDB entries were removed.
Hi Randy,
Indeed, true cases exist. I guess my shock that Nature still didn't retract the
paper and as a result of this the PDB didn't obsolete 2hr0 got the better of
me. This is not how science is supposed to work.
Cheers,Robbie
Date: Fri, 6 Feb 2015 11:16:48 +
From: rj...@cam.ac.uk
It looks a brilliant MR solution..
Do you know how you expect the A/B sets to pack?
This was always a problem with heamoglobin where the A B chains are very
similar ad form a tetramer, but we would group the solutions iinto sensible
tetramers (PISA will do that for you) and either set those
This is a famously fabricated crystal structure - the absence of
contact was one of the clues, see
http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html
Cheers, Matt.
On 2015-02-06 11:58, Kerff Fred wrote:
Hello,
Looking at structure 2HR0 (The structure of complement C3b
Hello,
Looking at structure 2HR0 (The structure of complement C3b provides insights
into complement activation and regulation. »,Abdul Ajees, A., Gunasekaran, K.,
Volanakis, J.E., Narayana, S.V., Kotwal, G.J., Krishna Murthy, H.M.;
(2006) Nature 444: 221-225), I noticed the absence of
Thanks for all the replies and sorry for rerun of a thread. I however have two
additional questions:
- Why is the pdb still available without any obvious sign of the fraud?
- Why is the paper stil available ?
Fred
-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des
I was about to complain that I have 14+ domains/ASU, but then I started
wondering—how on Earth did you do this sort of thing in the early days of
crystallographic software/structure? No PISA back then, and I imagine things
were far less automated…
JPK
From: CCP4 bulletin board
In our structures 1H6W (1.9Å) and 1OCY (1.5Å) we observed something similar, I
suspect the domain that makes the crystal contacts is three-fold disordered,
leading to layers of nothing. In our paper in JMB 314, 1137 (doi
10.1006/jmbi.2000.5204) we tried to explain it a bit, and describe what
Dear All,
I have a sca file. Will you please tell me by which software or how I can know
whether the sca file contains R-free tags? If not, by which software or how I
can add the R-free tags? And how much of the reflections I add the R-free tags?
I am looking forward to getting your reply.
Smith
Dave
Just for the record, the Wikipedia article you refer to is incorrect in
stating that 2HR0 (and possibly others) has been obsoleted: it has not (as
others have bemoaned!).
Cheers
-- Ian
On 6 February 2015 at 11:08, David Briggs drdavidcbri...@gmail.com wrote:
Haven'tthat paper and the
[ example structures with disordered crystal contacts ]
Yes and they all have a good bulk solvent correction.
-Bryan
Hi Faisal,
A lower R-free than R in the highest bin is not a big problem. The test set in
you highest resolution bin may be quite small which makes the values not so
reliable. Phenix uses different bins from what Refmac uses so you cannot
compare the values. If you performed your final
Hi Faisil,
Looking at your table, I think your data can go to even higher resolution than
you report.
Did you setup your data collection for higher resolution?
Cheers,
Scott
Scott T. R. Walsh, Ph.D.
Assistant Professor
University of Maryland
please report the bond length and angle rmsZ next to (or instead of) the
rmsd in Table 1.
'Instead' alone is also not enough - if in a normalized statistic you do
not know what you normalized against - that is, the variance or esd of the
target distribution - you do not know what Z means.
Hi Bernhard,
The rmsZ only says something about the deviations from 'ideal' values given
their esd. It is by no means a strong validation criterion. Values over 1.000
only say that your distribution is wider than expected (if you have no serious
individual outliers). So by changing target esds
Just to give a concrete example of Randy's point, PDB entry 2ts1 for tyrosyl
tRNA synthetase has layers of molecules with no contact between the layers.
This is because the domain (residues 320-419) that was providing the contacts
in this direction was disordered and could not be modelled
Hi Fred,
2015-02-06 11:58 GMT+01:00 Kerff Fred fke...@ulg.ac.be:
Hello,
Looking at structure 2HR0 (The structure of complement C3b provides
insights into complement activation and regulation. »,Abdul Ajees, A.,
Gunasekaran, K., Volanakis, J.E., Narayana, S.V., Kotwal, G.J., Krishna
Hi,
Another example is 2ZW3, again a membrane protein.
Best regards,
Takanori Nakane
On 2015/02/06 21:11, Adrian Goldman wrote:
Our recent membrane protein structure (4av3) doesn’t have much in the way of
contacts either, as is characteristic of type 1 membrane protein crystals.
Our recent membrane protein structure (4av3) doesn’t have much in the way of
contacts either, as is characteristic of type 1 membrane protein crystals.
Adrian
On 06 Feb 2015, at 11:51, Andrew Leslie and...@mrc-lmb.cam.ac.uk wrote:
Just to
One wonders if some of this structures might be good model cases for testing
issues like mask intrusion, missing Fpart regions, etc in order to improve bulk
solvent corrections….
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul
Paukstelis
Sent: Freitag,
Well maybe some pressure should be put on Nature to retract the article, so
that we can get the publication out of the PDB? It’s not good that it is there
for the unwary.
Adrian
On 06 Feb 2015, at 11:44, Folmer Fredslund folm...@gmail.com wrote:
6-Feb-2015
Dear Adrian
Maybe a petition could be circulated that many of us could sign requesting
Nature to retract this paper.
I don’t know if this has ever been tried, but my guess is that Nature would
take it seriously, especially
due to the overwhelming evidence that the structure was
We found something similar for a DNA quadruplex not too long ago (4U92).
This had surprisingly high resolution (1.5 Å) for having roughly half of
the ASU being disordered.
On 02/06/2015 06:51 AM, Andrew Leslie wrote:
Just to give a concrete example of Randy's point, PDB entry 2ts1 for
Let us know the ligand solubility in buffer solution used for the complex
formation!
The fact that your adding 0.05mM of even 10mM ligand in your solution does
not mean that you got that concentration in solution.
It is very likely often that the ligand bonds to protein the protein is OK
but the
Hi everbody,
I have one question with regards to the Bin R and Rfree values. My overall
R and Rfree values for (resolution1.4 angstrom) is 15% and 19%
respectively. But, the values in bin as shown in PDB header after the
refinement from the REFMAC are 15.7% for R and 14.5% for Rfree. In this R
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