Dear Ho,
On Fri, Feb 13, 2009 at 04:45:29PM -0800, Ho-Leung Ng wrote:
Can you elaborate on the effects of improper inclusion of low
resolution (bogus?) reflections? Other than rejecting spots from
obvious artifacts, it bothers me to discard data. But I can also see
how a few inaccurate,
Just to expand a little on the beam stop problem: the outlier
rejection algorithm in Scala ( I imagine in other programs) relies on
a consensus, that is it essentially assumes that the majority of
observations are correct (actually they are weighted by 1/
EstimatedVariance). This means that
Dear All,
A LABORATORY TECHNICIAN position is open at the Research Institute of
Molecular Pathology (IMP) in Vienna, Austria, in the Group of Dr. Peggy
Stolt-Bergner (http://www.imp.ac.at/research/peggy-stolt-bergner/)
We are seeking a scientific Technician experienced in molecular biology and
Dear guys,
Sorry for the off-topic question.
After I have solved my strucutre, I have found my target ligand bound at the
potential binding site. Also, I have
found that there are two more ligand molecules bound along the path from
solvent to the binding site. I think this
can enrich the ligand
Hi Keith,
I freezed my crystals with 35% PEG4000 as cryo.
They grow in 16% PEG4000, 4% Isopropanol, 0.1 M Na-Acetate. I just put the
hanging drop over 35% PEG4000, 4% Isopropanol, 0.1 M Na-Acetate and let it
equilibrate over night. They diffracted even better than with other cryos -
might be
Clemens, I know we've had this discussion several times before, but I'd
like to take you up on the point you made that reducing Rfree-R is
necessarily always a 'good thing'. Suppose the refinement had started
from a point where Rfree was biased, e.g. the test set in use had
previously been part
Hi all
I have two datasets of resolutions 1.6 and 1.65 Å both of the same molecule,
the problem that i am facing is the refinement.
The R factors are stuck at very high values 0.3329 and 0.3791 after
restrained refinement, although the the map fits into the electron density
very well.
Regards,
Dear bb,
can somebody explain to me the exact definitions for detector roll,
pitch and yaw? Can they be detector dependent or rather dependent on the
beamline setup? Is there a relationship with the goniometer position?
Many thanks in advance,
Jonathan
--
Jonathan Elegheert
Ph.D. Student
Dear Ian,
That was in fact one of my reasons for only calculating the free R
at the end of a SHELXL refinement run (the other reason, now less
important, was to save some CPU time). I have to add that I am no
longer completely convinced that I made the right decision all
those years ago. A
i have a density map and a model and i want to place the cofactor.
i use wincoot and find the electron density for the cofactor but...
how can i move the cofactor and play with it in this area?
Hi Rana,
Your email contains very little information which might help finding the
reason for the high R-values
- the resolution itself does not mean your data are of good quality. What
is the completeness (overall and high resolution shell), what are Rint/
Rsym and I/sigma? Maybe you are
Hi,
this is probably dependent on the integration program you are using -
there might not be one universal definition... did you compare the
programs' documentation?
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Mon, 16 Feb
Elad,
If it is only moving the coordinates of the co-factor and placing it in the
density,
once you load the coordinate file for your co-factor into the wincoot, it is
pretty much
drag and rotate process by using the option Rotate/Translate Zone
But if your question is with respect to playing
Hello all,
we have a dataset collected from multiple (2 or 3) parts of the same crystal
with a microbeam (20 micron). The merged data scales OK (not great) in
monoclinic (1-3% rejections). The resolution is 3.2-3.3 A, so the data is not
fantastic. This is the cell (similar for other
Dear George
I would still maintain that values of Rfree where the refinement had not
attained convergence are totally uninformative, so I would say you made
the right call! During a refinement run, Rfree is often observed to
fall initially and then increase towards the end, though usually not
Hi Jonathan,
Pitch, Roll and Yaw come from flight dynamics, see e.g.
http://www.answers.com/topic/pitch-yaw-roll.
With X parallel to the X-ray beam, Z pointing to the Zenith and Y being
perpendicular to X Y, they correspond to the roty, rotz and rotx
of the detector with respect to the
Yingjie Peng wrote:
..
After I have solved my strucutre, I have found my target ligand bound at
the potential binding site. Also, I have
found that there are two more ligand molecules bound along the path from
solvent to the binding site. I think this
can enrich the ligand to binding site,
Dear Yingjie,
I agree with Ed Berry that I do not believe that nearby binding sites
influence the Km (~Kd) which depend on bound and unbound concentrations.
However, there could be a strong kinetic effect, e.g. these secondary
binding sites could act as stepping stones when the path to the primary
Hi Bert,
It seems unikely you are experiencing merohedral twinning in your crystal
since none of your unit cell dimensions are equal length or integer
multiples. For your cell, you would expect to see multiple lattices. Is
it possible you have a dimer in the asymmetric unit? Strong NCS
Bert, Your self-Patterson peak may be real, i.e. you have pseudo
translation, which can then make the statistics *look* like the crystal
is twinned. Try a self-Patterson (perhaps sharpened) at somewhat lower
resolution, e.g 6 A. Maybe the peak is real, but is only 6% of origin
due to a slight
Dear all, deadline for submission of proposals for beamtime at BM14 (ESRF)
for the second run of 2009 [April/May] is this Friday, the20th February
2009. Beamline proposals can be submitted on-line from the BM14 webpages at
http://www.bm14.eu
PLEASE remember this call is distinct from ESRF
Dear Scientists,
It may be too much...
But as a biophysics student I would like to appreciate and feel happy to
have pdb
structures as my computers screen savers than to have some funny and fancy
stuffs.
And it may help me as a motivator to solve my own structures in future
I want to ask is
Hi,
You may want to have a look at
http://www.luminorum.com/html/luminorum_ltd___extras.html.
hth
Nadir
--
Pr. Nadir T. Mrabet
Cellular Molecular Biochemistry
INSERM U-724
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy
Hi all,
The resolution of my structure is 3.1A. There are three Mg binds in this
structure. I try to refine it with phenix. There are cleare extrea density
before I add Mg atoms. But when I put Mg in the central of density with good
coordination and try to refine it by phenix, those Mg move
Get a Mac, render some images in Pymol and run a slideshow with Ken
burns effect if you want.
Jürgen
On 16 Feb 2009, at 13:22, Jayashankar wrote:
Dear Scientists,
It may be too much...
But as a biophysics student I would like to appreciate and feel
happy to have pdb
structures as my
But as a biophysics student I would like to appreciate and feel happy
to have pdb
structures as my computers screen savers than to have some funny and
fancy stuffs.
And it may help me as a motivator to solve my own structures in
future
Hi,
I'm looking for a free program for calculating powder diffraction pattern,
given a PDB file. I googled for hours and only found a bunch of junks...
Thanks for your help!
Owen
On Feb 16, 2009, at 10:22 AM, Jayashankar wrote:
Dear Scientists,
It may be too much...
But as a biophysics student I would like to appreciate and feel
happy to
have pdb
structures as my computers screen savers than to have some funny and
fancy
stuffs.
And it may help me as a motivator
Dear All,
I have a question about the occupancy refinement of a ligand. I have a
dataset of 2.3 angstrom and the ligand binds in multiple conformations in
the active site.
My question is if it is possible to tell which orientation(s) has/have the
highest occupancy based on occupancy refinement.
Dear Ian,
I totally agree with your observations and recommendations. If one is
concerned about instability of the optimizer (minimization
and/or simulated annealing) I suggest to also monitor the value
of the total energy function (X-ray maximum likelihood term
plus all restraints).
Another
Dear Lisa,
you can specify custom bond and angle restraints by using the option
refinement.geometry_restraints.edits. Best is to save them to a file (e.g.
restraints_edits.params) and use this as input for your next
phenix.refine run. Assuming the ideal distance for your Mg is 2.1A and the
Hi Clemens,
Thank you for the clarification. I had thought you were
advocating using a general low resolution cutoff, with which I would
disagree. I spend a lot of time troubleshooting data collected and
processed by other people. Those are good reminders to go back and
check beamstop
Hi all
I am dealing with a protein which size is about 200kDa. Due to the impurity and
degradation problem, the protein has gone thru 3 purification steps (affinity
column ion exchange column gel filtration column). The buffer condition for
the last step of purification was 50mM MOPS pH7.0,
I just emailed the guy today and asked him if there was any hope of
getting an intel version in the future, and he wrote back almost
immediately and said he is working on it and is about 90% done. The
current one runs only on PPC.
I tried to hint subtly that it would be kind of cool to
Dear Owen,
The GSAS package can do that:
http://www.ccp14.ac.uk/solution/gsas/
It is important to put some values for the solvent contribution if you
want to get a meaningful pattern. Shout if you need a hand.
Good luck,
Jon
wob wrote:
Hi,
I'm looking for a free program for calculating
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