My personal experience is ( I frequently re-refine structures I cite
if all the data for that exist
in PDB) that PDB possesses a significant number of artifacts
unsupported by reality but by the wild imagination only. These
artifacts are originated from the modest, good and excellent
la
Hampton sells a Silver Bullets screen that may work for you.
ho
UC Berkeley
--
Date:Thu, 12 Mar 2009 12:15:18 -0700
From:Dinesh Palanivelu
Subject: Fragment Screening kit
--Apple-Mail-7-880081303
Content-Transfe
I like the standard Classics, PEGs 1 and 2, as well as the ProComplex screens.
We also use
Molecular Dimensions MemStart/MemSys and the Axygen High Probability Peg
Screen. Good
luck.
Franz
On Thu, 12 Mar 2009 16:03:10 -0400, JOE CRYSTAL wrote:
>Sorry for the off-topic subject. I am new to
The deadline for the may/June cycle of general user time for PX in the
ALS is coming up soon (This Sunday).
The Berkeley Center for Structural Biology (BCSB) has recently
completed a number of upgrades:
Sector 8: Recent improvements include:
* A high-accuracy microdiffractometer on BL 8.2.
Current version does not expand data or model. C222 twinned in P2 will
not be handled if data are in C222.
Overmerged data are a bit tricky to deal with. And model in higher
space group would not fit into the asymmetric unit in general.
In short: in the current version space group should be a
Dear Mark
Stay calm
Buzz-words come and very frequently do not stay, they go away with
the artifacts they advocate...
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica
Hi Pavol, Garib
Actually, that bit of doc doesn't answer a few practical questions we
keep running into:
1) What spacegroup should you provide the data in? The usual scenario,
in practice, is that one merges in too high symmetry, and wants to check
whether it is actually lower symmetry with
Dear Dale,
> 1) There is a need for additional validation of structure factor
> depositions.
>
>My recollection is that the output of SF Check is available to
> the depositor via ADIT on the RCSB site. I have found that report
> to be quite helpful in checking for gross errors in my stru
Sorry for the off-topic subject. I am new to membrane proteins. We already
have Qiagen MB class I and II, Sigma Membrane, and Membrane Gold kits, but I
want to know if there other kits out there you would recommend. Thanks a
lot,
Joe
Dear all,
We have been trying to crystalize a membrane protein in which the
function is unknown. We got some initial crystal hits and we are in
the process of optimization.
I am looking for a screening kit for identifying the potential ligand/
substrates (small molecule metabolites) of an unk
Dear Dale,
On Thu, Mar 12, 2009 at 11:07:05AM -0700, Dale Tronrud wrote:
>This thread has evolved into two different topics. Just to
> clarify:
>
> 1) There is a need for additional validation of structure factor
> depositions.
>
>My recollection is that the output of SF Check is
On Mar 12, 2009, at 9:01 AM, Andreas Förster wrote:
Every night I pray to a different god for version 2.4 to actually
work.
Prayer might be making it worse, depending upon the wrath and
vindictiveness of the imaginary deity of choice:
http://www.nytimes.com/2006/03/31/health/31pray.html
Hi Dale,
1) There is a need for additional validation of structure factor
depositions.
PHENIX has tools for this:
1) "phenix.cif_as_mtz" will convert the PDB data file with diffrcation
data into MTZ file. It automatically will figure out if the data are
X-ray: Iobs or Fobs, or Neutr
Dear Frank,
Thank you for your answer, as unimitable as ever. We do of course have
to wash one plate at a time when we each feel the pinch of hunger; but as we
do so we should not forget that the PDB is the Central Planning Office, and
that the order for that industrial-scale dishwasher has t
This thread has evolved into two different topics. Just to
clarify:
1) There is a need for additional validation of structure factor
depositions.
My recollection is that the output of SF Check is available to
the depositor via ADIT on the RCSB site. I have found that report
to be qui
Dear All,
I would like to inform you that two SG centers:
Center for Structural Genomics of Infectious Diseases - CSGID
http://www.csgid.org
and
Seattle Structural Genomics Center for Infectious Diseases - SSGCID
http://ssgcid.org/home/Target_Status.asp
set-up the server at University of Virg
Dear All,
a News & Views article in Nature 458, pages 37-38 of 5 March 2009
(link below) states:
"The development of structural biology WAS historically based on the
principle of divide and conquer — individual proteins were purified to
homogeneity and their atomic structures were solved in
Gerard Bricogne wrote:
Looking forward to the archiving of the REAL data ... i.e. the images.
Using any other form of "data" is like having to eat out of someone else's
dirty plate!
That may be so -- but if I'm hungry now, I just pop it in the sink -- I
don't publish a call for tenders o
William G. Scott wrote:
On Mar 11, 2009, at 8:49 PM, Raja Dey wrote:
Dear Friends,
2. If I update X11, whether it will cause any problem to the existing
programs?
You run the risk of having them work,
This risk is marginal. The current 'stable' xquartz 2.3.2 still
flickers the hell o
Dear Gerard and all MX crystallographers
As I see there are two problems.
1) Minor problem: Sanity, semantic and other checks for currently
available data. It should not be difficult to do. Things like I/sigma,
some statistical analysis expected vs "observed" statistical behaviour
should so
Dear Eleanor and Gerard,
PDB testing is performed on MTZ file and can not detect conversion
errors.
Wladek
At 10:03 AM 3/12/2009, Gerard Bricogne wrote:
Dear Eleanor,
That is a useful suggestion, but in the case of
3ftt it would not have
helped: the amplitudes would have looked as healthy
Eleanor,
Please note that so far CIF structure factors files were not sent by
deposition site for verification to authors.
I spoke with Helen and John last Saturday and they promised me to change
that policy. Alternatively, one can check his/hers new deposit on every
Wednesday morning.
Best r
CALL FOR ESRF SYNCHROTRON BEAM TIME WITH ONLINE
DEHUMIDIFIER AT BEAMLINE ID14-2
Proposal Submission Deadline: 31st March 2009
Beamtime will be available from the 14th to the 17th M
Dear Kim,
yes, Refmac handles pseudo-merohedral twinning. The procedure is fully
automatic and there is not much to change but the documention can be found
here:
http://www.ccp4.ac.uk/html/refmac5/keywords/keywords_5_5.html#Twin
Pavol
Just to second this, and point out that with Mingw cross compilers, you
can build Windows executables on Linux or OSX that run on all versions of
Windows from 95 to Vista... (and might even run on 3.1, but I don't have a
3.1 box to test on).
> Have you considered gcc under MINGW? It produced more
Hi,
I am currently trying to work with perfectly twinned data and have a starting
model that I found through phaser. In trying to refine the model against the
data, I noticed that Refmac5 has a "twin refinement" option that performs some
sort of automatic refinement against the found twin laws
Dear Eleanor,
That is a useful suggestion, but in the case of 3ftt it would not have
helped: the amplitudes would have looked as healthy as can be (they were
calculated!), and it was the associated Sigmas that had absurd values, being
in fact phases in degrees. A sanity check on some (recalc
Hi Bernhard
Did you try this:
http://download.corruptedfilerepair.com/post/2008/07/02/clexe-Download-F
ile-clexe.aspx
(note that after clicking on the "Download Link #7: Download CL.EXE"
link, the actual download link in case it doesn't start automatically,
which it didn't for me, is below the a
Have you considered gcc under MINGW? It produced more stable
code that runs under more versions of windows than CL.
=
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd
I presume you have done density modification after calculating the exptl
phases?
If you use REFMAC to refine your partial model with the exptl/density
modified phase restraints your FWT PHWT fourier coefficients already use
the combined phase.
I am not sure how to choose a damping factor. If y
It would be possible for the deposition sites to run a few simple tests
to at least find cases where intensities are labelled as amplitudes or
vice versa - the truncate plots of moments and cumulative intensities at
least would show something was wrong.
Eleanor
Wladek Minor wrot
Dear All,
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