Check your mosflm input file.
If this is an ADSC type detector and you have specified that it is
(using DETECTOR TYPE ADSC or SCANNER TYPE ADSC), but have not
explicitly specified the overload limit with OVERLOAD CUTOFF, then the
default overload cutoff for integration will be 100,000, and
The H+-ATPase from A. thaliana had anisotropic diffraction (ca.
3.6/5.5Å). This could be explained by the crystal packing and more
specifically the detergent micelles in the packing.
See:
Pedersen BP, Buch-Pedersen MJ, Morth JP, Palmgren MG, Nissen P. Crystal
structure of the plasma membrane
Hi, for an analysis I need the sequence identity of any PDBid to its
closest match in the PDB *at the time it was deposited*.
It seems like something somebody would have done before; any thoughts
where to find it?
Cheers
phx
Hi
I'd be somewhat surprised if this accounted for the difference since
it would require the routine collection of many overloads in each
dataset before you'd notice that the completion was higher
systematically.
(The two different cutoffs that James refers to are the absolute
cutoff
Also, if you happen to use refmac for refinement: it rewrites LINK
records as LINKRs in the output pdb file -- and LINKR records are
unknown to Coot...
JED.
--
AstraZeneca UK Limited is a company incorporated in England
Hello,
Could you please help me with the sketcher?
I'm trying to use ccp4 sketcher to generate a new ligand and then complex it
with a protein in coot. I've drawn the ligand, numbered each atom and
defined each bond type. Then I ran save file, create library description.
The pdb file was loaded
This is a REAL PAIN Paul!
Eleanor
Debreczeni, Judit wrote:
Also, if you happen to use refmac for refinement: it rewrites LINK
records as LINKRs in the output pdb file -- and LINKR records are
unknown to Coot...
JED.
Can you send your fragment of the pdb containing the ligand, and the cif
file?
Eleanor
Yahui Yan wrote:
Hello,
Could you please help me with the sketcher?
I'm trying to use ccp4 sketcher to generate a new ligand and then complex it
with a protein in coot. I've drawn the ligand, numbered
LINKR is not part of the PDB format:
http://www.wwpdb.org/documentation/format23/sect6.html
It's also not supported by MMDB, for that reason. I think Eugene put in
some stuff to store remarks, but I don't know if unrecognized keywords
are also stored (Eugene?). So there's a problem here, and
Rashmi,
To facilitate dissolution of a peptide we found ultrasound (in glass, plastics
absorb much of the energy) useful. It might be also helpful to warm the
solution mildly.
Frank
Hi Yahui!
I am having this problem as well again and agin. Most problematic is it,
if you have non-standard atoms in your compound.
I don't really know whrere the problem lies, but here is what I do:
Do not use sketcher!
Simply generate your ligand using coot by placing atoms into the density
Hi Yahui!
I am having this problem as well again and agin. Most problematic is it,
if you have non-standard atoms in your compound.
I don't really know whrere the problem lies, but here is what I do:
Do not use sketcher!
Simply generate your ligand using coot by placing atoms into the density
Perhaps you could try to use JLigand. It may do a better job. it is
available from:
www.ysbl.york.ac.uk/mxstat/
In the jligand session there are two tutorials also. they may help you
to run and generate your ligand description.
If any problem please let me know.
In general refmac is not
In the latest, latest version refmac writes LINK instead of LINKR. It
is a temporary solution. We need a better solution and hopefully we
will have one soon
This version of refmac is available from:
www.ysbl.york.ac.uk/refmac/data/refmac_experimental/
regards
Garib
P.S. This version also
Dear All,
I was wondering if anyone has compiled a list of common proteins that can
co-purify from E. coli preps (and yeast etc), and crystallize instead of the
protein of interest. If list members send me individual examples I will compile
a summary for the bulletin board.
best wishes
Hi,
I also have a question concerning anisotropic data. Collected a data set and
the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A).
So my first question is how to handle these data. I got only experience with
normal data using the ccp4 suite. Are there any
On 9 Jun 2010, at 12:54, Murray, James W wrote:
I was wondering if anyone has compiled a list of common proteins that can
co-purify from E. coli preps (and yeast etc), and crystallize instead of the
protein of interest. If list members send me individual examples I will
compile a summary
But does it follow the PDB format for LINK records; it is a disaster if
the LINK read from the PDB have a different definition and information
content than LINK records output from REFMAC. At least LINKR is a
flagged non-standard record.
Eleanor
Garib Murshudov wrote:
In the latest, latest
A first concern with that extreme anisotropy is at the integration and
scaling stages.
Large swaths of your detector are empty of reflections, but they will still
bias the way reference profiles are calculated at integration; while the
lots of reflections with intensities around 0 (but with
Anisotropy in the diffraction pattern could simply be due to the shape of the
crystals. The intensity of diffraction is a function of the volume of
diffracting matter that is hit by the X-ray beam. Think for example of a thin
plate crystal, which you rotate in the X-ray beam. When the plate is
Hello Garib,
I just tried JLigand. It's amazing. I opened the pdb file which was made by
sketcher and save lib file and coordinate file. Then load these files to
coot. Everything works fine now. I think I need to double check the ligand
as you advised.
Thanks a lot to you all.
Regards,
Yahui
Although Bill his as a the return address to his message, it seems to me to be
of considerable relevance to the crystallographic community as a whole. My
recent experience representing the ACA on the AIP Governing Board and Executive
Committee provided considerable introduction into many of the
Hi
Many years ago I coded up integration using anisotropic resolution
limits for Mosflm - it seemed to work well, but the refinement
programs available at the time really didn't like huge regions of
reciprocal space having no data in them - they preferred to have
measurements there with
Dear Marie,
I believe that the first of Fred's explanations can mostly be corrected for by
scaling (and it could partly be overcome by longer exposure times as long as
radiation damage does not kick in).
In your case, where one cell axis is about 10x as long as the other two, Fred's
second
I suggest using the PRODRG Server: http://davapc1.bioch.dundee.ac.uk/prodrg/
On Wed, Jun 9, 2010 at 7:22 AM, Matthias Zebisch
matthias.zebi...@bbz.uni-leipzig.de wrote:
Hi Yahui!
I am having this problem as well again and agin. Most problematic is it, if
you have non-standard atoms in your
I guess then Fred's reply part one explains everything :-)
Jürgen
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:
NIH funded Postdoctoral Fellowship, structural biology
Cell Biology and Biophysics Unit, National Institute of Neurological Disorders
and Stroke (NINDS)
Location: NIH Main Campus
Start Date: position available immediately
Postdoctoral positions are available in the Cell Biology and Biophysics
NIH funded Postdoctoral Fellowship, structural biology
Cell Biology and Biophysics Unit, National Institute of Neurological Disorders
and Stroke (NINDS)
Location: NIH Main Campus
Start Date: position available immediately
Postdoctoral positions are available in the Cell Biology and Biophysics
Frederic VELLIEUX wrote:
Anisotropy in the diffraction pattern could simply be due to the shape of the
crystals. The intensity of diffraction is a function of the volume of
diffracting matter that is hit by the X-ray beam. Think for example of a thin
plate crystal, which you rotate in the
I vaguely recall an email from Kay Diderich about 3 years ago to this board but
I couldn't find it, describing a neat method of distorting the diffraction
image to meet the ellipsoidal characteristics of the anisotropic diffraction.
But I might be confusion myself, anyhow Kay can you comment on
Hi,
I suggest you to try HADDOCK if you have some interaction data, such as the
binding site, key residues, etc. It can use the interaction data as a
restrain and make the dock more accurate. And the web interface of the
HADDOCK server is very easy to handle.
Best wishes.
On Tue, Jun 8, 2010 at
On 09/06/2010 16:49, James Holton wrote:
Operationally, I recommend treating anisotropic data just like
isotropic data. There is nothing wrong with measuring a lot of zeros
(think about systematic absences), other than making irrelevant
statistics like Rmerge higher. One need only glance at
Hi all,
I've posted this in the hope that somebody in the CCP4 community may
have come across this problem and can shed some light. I've posted this
question on other lists (cnsbb, ccpnmr and aria - the reason will become
clear), but with no success so far.
I have recently acquired a
Frank von Delft wrote:
On 09/06/2010 16:49, James Holton wrote:
Operationally, I recommend treating anisotropic data just like
isotropic data. There is nothing wrong with measuring a lot of zeros
(think about systematic absences), other than making irrelevant
statistics like Rmerge higher.
I have often wondered how it is that one can actually run and play games
like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of
the EPROM cartridges that I used to put into my Atari 2600 (circa 1982),
but for some reason programs written just a few years ago will neither
But at some point, getting a clear map might not be the goal. If you're in refinement mode, the weak reflections also provide information that your model needs to fit. I find I/sig(I) (or I/sig(I)) to be about as useful as
Rmerge (or its relatives). Ron
On Wed, 9 Jun 2010, James Holton
My sincere apologies for not being clear. When I said gcc, I meant I installed
the full compiler package which includes gfortran. I did use gfortran for the
compilation. I have also tried the commercial Intel compilers (albeit the
evaluation version), which produced the errors I described
On Wednesday 09 June 2010 10:45:07 am James Holton wrote:
I have often wondered how it is that one can actually run and play games
like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of
the EPROM cartridges that I used to put into my Atari 2600 (circa 1982),
but for some
Hello Ethan,
I may be mis-remembering, but I have it in mind that the cns source code
requires selecting or porting a set of compiler-specific routines in one
of the source modules. These are work-arounds for the variability in
Fortran implementations mentioned above.
The CNS build system
Please note that the latest version of Xcode in Mac OS X 10.6.3
breaks the Intel Fortran and C compilers. It is possible that Xcode also
breaks gfortran, but I haven't tested it. I've reverted to the
Xcode version that came with the original Snow Leopard release.
Intel is aware of the problem,
Hi All,
As I've said, I'm trying to put some version of Linux on an old SGI O2. I have
found a couple of versions of Linux that I'd like to try but I think the
problem now might be that the O2 isn't configured to read from CD ROM on start
up. Does anyone know how to go about changing this
Hello,
I have tried HADDOCK recently and have got some parsing related error!
(indicative of some errors in the input PDB files.). I have checked my pdb
files and did not figure out anything wrong.
May I please get some suggestions about it from any of the experienced ones in
this area?
I am not sure what is the problem you have. Usually, I use O formated PDB
files. It works well.
I think you can report your bug to the Dr. A.M.J.J. Bonvin who is
maintaining the server.
On Wed, Jun 9, 2010 at 6:08 PM, anil kumar anilkumar...@yahoo.co.in wrote:
Hello,
I have tried HADDOCK
Hi all,
Thanks to everybody who has contributed over the past couple of days on the
various bulletin boards I have posted to. As is always the case, the solution
was quite simple but completely passed me by. I'm going to use Mac inexperience
as an excuse here... :-)
So the original problem
A PS on the Intel compiler / Xcode issue: the first work-around
(-use-asm) does not work in conjunction with OpenMP enabled. Thus,
I recommend to revert to Xcode 3.2.1 (and then reinstall the
compilers) until the issue has been fixed by Intel.
Axel
On Jun 9, 2010, at 5:19 PM, Patel, Pryank
On Tue, 8 Jun 2010 21:50:10 -0700
William G. Scott wgsc...@chemistry.ucsc.edu wrote:
Sorry about the off-topic nature (so to speak) of this post,
especially given that it is not yet Friday, but I am interested what
our community thinks of this:
Thank you Rotem and everyone else who replied to mypost. I am replying to
Rotem's mail as his link has everything inclusive of what others had
suggested.
I love ccp4 bb
You always get more than what you ask for.
Thanks guys.
Ivan
On Tue, Jun 8, 2010 at 10:41 PM, Rotem Sertchook
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