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,
See the list in the following link
http://bip.weizmann.ac.il/toolbox/structure/binding.htm#pp
Good Luck
Rotem Sertchook
On 8 Jun, 2010, at 21:59, xaravich ivan wrote:
Dear CCP4 users,
Though this is not directly linked to ccp4, i bet many of you have
solved crystal structures of the ligand a
Hi folks:
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:
http://library.ucsc.edu/sites/default/files/Nature_Faculty_Letter.pdf
Something similar happened with UC and Cell Press a fe
Hi Ivan,
Recently I used PatchDock (http://bioinfo3d.cs.tau.ac.il/PatchDock/index.html)
to find interface between two proteins.
Good luck,
Biswajit
Dr. Biswajit Pal, Scientist,
Centre for Cellular and Molecular Biology, E009,
Uppal Road, Hyderabad - 500 007, India.
Phone : +91-40-2719-2831,
Fax :
Hi,
We are using a modified version of ISFM with 10 g/L glucose, based on
a paper by Maiorella et al. from around 1988 or 1989. This is a
medium that is based on IPL-41, which we purchase as a powder, and
supplemented with ultrafiltered yeastolate and lipids. It is
completely protein-free. It i
Dear All,
Filip and I have arranged for him to present the issue of
EM data deposit policies at the USNCCr meeting on Fr before the
ACA meeting in Chicago. If anyone has suggestions/ideas that
might be worthwhile a discussion at that policy meeting, please
let Filip or me know.
The National Acade
Briefly (and top-postingly),
Coot does not draw covalent bonds between non-tandem residues.
Coot will represent LINK records if they are in the PDB file.
Coot will respect the links generated by JLigand if you try to do sphere
refinement.
The Coot <--> JLigand internface will improve in th
Hi Sean,
do the ligand and the Thr belong to the same chain, and did you check that the
distance between the bonding atoms is not beyond coot's cut-off?
Tim
On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote:
> I have used JLigand v 0.2.1 to create a link between a Thr residues and
> a c
Hi Ivan,
you find a compilation there:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Bioinformatics#Docking
hth
guenter
Dear CCP4 users,
Though this is not directly linked to ccp4, i bet many of you have solved
crystal structures of the ligand and receptor separately and tried to do
http://rosettadock.graylab.jhu.edu/
Good luck !
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: +1-410-6
Dear CCP4 users,
Though this is not directly linked to ccp4, i bet many of you have solved
crystal structures of the ligand and receptor separately and tried to dock
it. is there any program that docks two protein molecules. We have an
overall idea where the protein will bind to the receptor. Is th
I have used JLigand v 0.2.1 to create a link between a Thr residues and
a covalent adduct. The adduct refines well and shows up as a covalent
bond in PyMOL. However, when I'm in Coot there is no bond present
between the Thr OG1 and the ligand. I've loaded the Jligand link.lib
file that I create
Dear All,
Thank you for your help! There do have something needed to be checked
carefully, as you suggested. Peter Zwart
showed me the right way of explore_symmetry_metric, which indicated there is
some relationship between the two
unit cells. I hope it can explain the strange wilsonB and fa
Hello,
I am working on a protein whose EM model has been built long time ago.
The crystal structure has been solved recently and I want to know the
difference between the crystal structure and EM model. Unfortunately
there is no data in the EM data base, so I can not use Chimera or Phaser
to
Dear everybody!
I am currently having an issue with anisotropic diffraction and would
like to cite some references.
I am sure there are plenty of examples outthere.
So, if you are having an own published example at hand, can you please
send me the reference and
maybe the diffraction limits a
I don't know. Which reflections are missing? Strong ones, weak ones, near the
rotation axis ... ?
Phil
On 8 Jun 2010, at 14:27, Simon Kolstoe wrote:
> Thanks Tim, Phil and Andrew for your answers.
>
> Just one further related question:
>
> Why is it that mosflm seems to report higher complete
Thanks Tim, Phil and Andrew for your answers.
Just one further related question:
Why is it that mosflm seems to report higher completeness than XDS on
the same data (I've seen this on about 50 datasets)? I always thought
it was due to mosflms peak extrapolation but it seems this isn't the
Oliver,
first, what is the source organism of the protein, human, dog, cat, insect, or
bacterial?
second, how big is the native protein, and how big are the tags you've added?
third, how many transmembrane spans are predicted (use any of the million
programs available)
fourth, when you seperate t
Hello All,
This maybe of interest to people working with complementary techniques to PX.
We are hosting the Annual Analytical Ultracentrifugation Workshop and
Conference on 12th-16th September 2010 at the Park Plaza Hotel in Nottingham,
UK.
This will consist of:
(i) Software and AUC workshop (12t
The easy Q first:
Wilson plot B values are very unreliable for 4A data - b=20 is almost
certainly wrong, but until you have a model to refine it is hard to get
a proper estimate.
Q2: With a decent model the ligand should show up as a blob, even at
this resolution. You might have trouble fi
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