Dear CCP4 users,
We have an opening at the ESRF Macromolecular crystallography group
(http://www.esrf.fr/UsersAndScience/Experiments/MX) for a Post-Doc to
work on *the role of membrane proteins in the resistance of
*/Deinococcus radiodurans/* to extreme conditions (see advert below).
The E
As written in
Jovine, L., Djordjevic, S. & Rhodes, D. (2000). “The crystal
structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by
Mg(2+) in 15-year old crystals” J Mol Biol 301, 401-414.
"Furthermore, the possibility of a Mg2+-catalysed cleavage of the
phosphodiester bond
Dear Xie,
you need to use the right columns for calculating maps. From your
description it seems you could do the following in FFT:
a) map after density modification:
F1=Fobs PHI=PHIDM W=FOMDM
or (DM should write out these columns as well):
F1=FDM PHI=PHIDM
See: ht
Thank you very much for this clear and long answer, Dale. You gave me
exactly the information I needed.
Thanks again having taken the time to answer to my questions.
Cheers.
Peter
On Thu, 5 Feb 2009 14:51:15 -0800, Dale Tronrud
wrote:
> A map file stores a density value for each point on a g
Please find attached an advert for a short Marie-Curie fellowship at the
National Hellenic Research Foundation, Athens, Greece.
We seek to recruit a biology/biochemistry graduate, with not more than 4
years of research experience at post-graduate or equivalent level, who
will be trained by res
FWIW, many of the crystals used in "classical" neutron diffraction
experiments were pretty elderly samples by the time data collection was
initiated, partly to allow large crystals to grow ever larger, partly
because of the mandatory deuterium exchange process and partly because the
experiments las
I am told by a mentor that rigid body refinement should never be the last
refinement before submission to pdb. Any idea why? Structures in which every
round of retrained refinement messes up a conformation, is there any
alternative to not using rigid body refinement?
Andy
Hello,
I was using the TLS Create/Edit module to create a TLS file from scratch. In
the module I ran it once but wanted to change some parameters. While I had the
module interface still open, I selected to delete the TLS project entry just
made in the list of jobs. When I did this I did not
Andy,
you should probably direct this question to the mentor first. What is
her explanation?
What do you mean by "refinement messes up a conformation"? Sometimes
with poor quality data refinement might lead to poor Ramachandran map.
You fix it manually, only to see it deteriorating again. You
On Feb 6, 2009, at 15:58, Andy Millston wrote:
I am told by a mentor that rigid body refinement should never be the
last refinement before submission to pdb. Any idea why?
When restrained refinement 'messes up a conformation' it is extremely
likely it does it for a perfectly sound reason.
On Feb 6, 2009, at 6:58 AM, Andy Millston wrote:
I am told by a mentor that rigid body refinement should never be the
last refinement before submission to pdb. Any idea why?
It is counter-productive and he/she doesn't want to get jumped and
beaten up in the parking lot at the next conferenc
For a counterexample, from Iwata's group,
Horsefield et al. Succinate: quinone oxidoreductase Acta. Cryst.(2003). D59,
600-602:
"It proved critical to freeze the crystals within 72 h of crystallization set-up. Crystals that were frozen after this time limit
showed no diffraction. This alteratio
Thank you for your responses.
Restrained refinement does a good job at refining most of the structure except
a small region with poor density. Every time I refine it, it puts this region
completely out of the map. It doesn't have much effect on overall geometrical
factors as its a very small pa
Hi Andy:
Just be very careful of special pleading type arguments. I really
think this is trying to tell you something, along with the
Ramachandran plot. On a more practical level, the PDB will flag it
when you try to deposit it. There is something wrong.
It might be worth making a comp
Hi,
On Fri, Feb 06, 2009 at 08:13:29AM -0800, Andy Millston wrote:
> Restrained refinement does a good job at refining most of the
> structure except a small region with poor density. Every time I
> refine it, it puts this region completely out of the map.
Do you mean:
a) after restrained refi
I have to second that.
I recently had crystals that will only grow after seeding and will live
for exactly five days. On the sixth day, the same drop will have tracks
of dissolved crystals left in every drop: they almost look like tire
tracks. The crystals frozen on the fifth day diffract to 2.
Dear SLS users,
Next call for proposals for the non-PX beamlines of the Swiss Light Source, SLS
will be launched on the 8th of February, 2009.
Deadline for proposal submission: Sunday, March 15, 2009
Submission: All submissions will be handled by the SLS Digital Users Office
(DUO) /contac
Dear Colleague:
You and your colleagues are cordially invited to join us for the 14th
Annual Structural Biology Symposium to be held at the University of
Texas Medical Branch at Galveston on March 27th, 2009. The meeting is
organized by the Sealy Center for Structural Biology & Molecular
Biophysi
We have a hi prep SP column from GE. We try to load ~14 mg protein but all
goes to FT. We lowered the pH and changed the buffer but no luck. We would
appreciate all suggestions. Mike Colaneri
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