Is there any parameter which i had to check.
Yes, the contour levels of your mFo-DFc map...
(My guess is that you are contouring at an arbitrary low level - say, 3
sigma.)
--dvd
**
Gerard J.
The obvious Q is whether there is some additive in the crystallisation
or cryo which could be showing up in the maps..
But in such a high symmetry space group is it possible that the blobs
are on some symmetry axis? I sometimes observe awful holes or peaks on 3
fold axes, where I think any
As Eleanor says, errors in an electron density map tend to accumulate on
special positions, i.e. on rotation axes (there are plenty of them in
F432). There are statistical reason for this and the effect is often
observed in small molecule crystallography. In such cases attempts to
put atoms (e.g.
Dear All
hopefully there will be a live stream of this years events (weather permitting
as the UK is suffering travel restrictions due to snow and ice) at
http://extrplay.dl.ac.uk/
the session links should go live about 15 minutes before the session begins
Charles Ballard
CCP4
--
Scanned by
A good place to start is P. Müller, S. Köpke and G. M. Sheldrick
(2003) Is the bond-valence method able to identify metal atoms in
protein structures? Acta Cryst. (2003). D59, 32-37[
doi:10.1107/S0907444902018000 ]
Cheers,
Stephen
2010/1/5 Clayton, Gina Martyn gina_clay...@merck.com:
Rajan,
I'll second what Eleanor and George have said - high symmetry space
groups with noisy Intensity measurements (perhaps it was a weak data set
with high Rmerge?) really exaggerates the amount of garbage that you
see in the maps.
Cheers-
Steve
From:
Dear ccp4bb
A structure I have recently finished has a cavity with four waters in
it. I am wondering if I might be able to fit a small molecule in the
same place. Does anyone know a way of making some type of map of this
cavity and then searching through a small molecule library to see
Rajan,
Likely you have the habit, like me and I suspect most people, to
contour difference maps at +/- 3 sigma. In the beginning of
refinement, these difference map will have significant peaks at 3
sigma, i.e. positive peaks were there is nothing and there should be
atoms and negative
If I remember correctly, arp/warp and/or phenix/resolve can do something
of that kind. Did you check the documentation of these programs?
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Wed, 6 Jan 2010, Simon Kolstoe wrote:
Dear all,
See below a post-doc position available at the Institute of cancer
Research posted on behalf of my colleague Bissan Al-Lazikani which
might be interesting for someone with a structural background. Please
don't reply to me.
Rob van Montfort
The Institute of Cancer Research (a
In addition to what the others have mentioned, if you're curious about sigma
levels to contour you may want to deliberately omit
an atom from your structure (say an ordered oxygen in a good portion of the
structure) - the height of the difference density peak would be meaningful
and you then could
This is just to remind you, after the holidays, that the deadline for the
applications is approaching...
=
Practical workshop on the use of longer wavelengths in Structural Biology
*The routine accessibility, on some macromolecular crystallography (MX)
beamlines at SR sources, of
Hi,
I agree, that dissimilarities in residues will propagate error in the model.
But, at the same time more similarities supposed to increase the quality of the
model. Similarities and identities between A and B and also between B and C are
more than that between A and C. Dissimilarities are as
The SDsearch software is used to search compound libraries in the form
of SD files over chemical properties and chemical substructures.
SDsearch 2.0 now adds multi-conformer docking to check the steric
compatibility of compounds that contain positioned subfragments within
protein target sites.
Hi Simon,
I suggest docking with the free web service DockBlaster:
http://blaster.docking.org/start.shtml
DockBlaster runs DOCK 3.5.54 and gives you the freedom to dock any molecule
you want into your structure.
Check out this page for more information:
Hello,
In order to process things in parallel I developed a simple
tool to run (for the moment) parameter sweep applications.
I.e. you want to run many times the same program with only
different input parameters.
It can be used to parallelize execution on a multi processor
machine or even to
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