Dear colleagues,
it appears that following the rejection of the software patent directive by
the European Parliament there is now another attempt going on to get
software patents consolidated, this time through the back door.
Since the threat of software patents is relevant to the
We are pleased to announce the release of TARDIS v2 beta at
http://pxgrid.med.monash.edu.au:8000/
TARDIS v2 provides a central, searchable index for federated raw
crystallography data.
Improvements over TARDIS v1 (http://tardis.edu.au):
- Data is no longer stored in a Fedora Digital
Dear all,
please excuse the non-CCP4-related question, but maybe there is someone
out there who can help us.
We are trying to find a recipe for making REALLY good chemically
competent E. coli for our local cloning facility. What we would like to
have is more or less:
- 109 cfu/ug DNA
-
Dear Wulf.
we have relatively good results using the method of Inoue (described in
Sambrook and Russell) for the production of chemically competent cells. As
strain we use quite often E.coli DH5alpha (blue/white cloning possible).
It is really difficult to get a cfu of 109 but 108 up to
*Second Announcement
EMBO / MAX INF2 2009 a Practical Course on*
*Structure Determination in Macromolecular Structure*
ESRF-EMBL, Grenoble, France, 15 - 19 June 2009
The EMBO / MAX INF2 2009 course on Structure Determination in
Macromolecular Structure will be hosted by the ESRF in Grenoble,
Two suggestions...
Check that the coordinate fields in your pqr file are separated by
spaces (some pdb to pqr converters don't always do this in my hands,
probably due to large negative coordinate values). Also, try using your
.pqr file and .in file to run apbs from the command line and see if it
Hi.
Does anyone have experience using solutions containing manganese as
crystallization buffers (buffers, not screening well solutions)? The
protein that I am working requires manganese for activity, and I have read
reports of related proteins crystallizing in manganese buffers. I made a
buffer
Hi,
I think that this is related to general pymol problem in ubuntu 8.10.
We had exchanged couple emails with Warren about this but I have not
heart back from him since.
It seems that there is a bug in pymol or Tkinter library and whenever
pymol tries to open special kind
of window it crashes
Presumably you want Mn2+ , but you need to specify.
If so, you need to make it up fresh, and keep it at a pH below 7 if at
all possible, as it oxidizes readily.
Bis-tris will weakly chelate it and slow the oxidation process.
On Apr 6, 2009, at 11:14 AM, Matthew Alan Bratkowski wrote:
Hi.
Dear Matt,
I use manganese for all my kinase buffers. My holobuffer contains 2mM
manganese at pH 7.0. The key was to add manganese after you pHed the
buffer with NaOH. I never used any basic buffer and it could be issue
if your buffer is too basic. Below is the recipe for my holobuffer. I
Dear All,
I have a crystal growing in the presence of 0.1M Sodium Acetate pH 5.0, 10%
PEG4000, 7.5% Dioxane and 10% Ethylene Glycol. I wanted to know if it would
be alright to use Samarium chloride for derivatization. I am worried about
the leaching of samarium by acetate. Also, what soak times
We regularly use 1-2 mM Mn2+ in xtal set-ups. The problem we've
encountered is formation of the insoluble, brown-colored Mn(OH)2 in
more basic solutions, but we've also found that the Good buffers
(HEPES, EPPS, etc.) are less prone to the formation of the
precipitate, while Tris seems to
I have used up to 20 mM MnCl2 in acidic buffers without visible changes in the
color of the solution. Unfortunately it changes quite dramatic above pH of 7-
Probably due to the formation of Mn(OH)2, which Arthur already mentioned. It
might be further oxidized to a Mn3+ species.
During a
Hi all,
I have an interesting problem case at the moment.
We have crystallized the same 2-domain protein in two different,
i.e. non-isomorphous, crystal forms.
There is a decent homologous structure for one domain
(about 40% of the total), but no known homologous structure for
the larger second
Hi Ethan,
give Eden a chance. It's a pain to get it running but once you've
overcome memory addressing issues it runs like a dream and
significantly improves your remaining electron density map. Or if you
are not that desperate yet you could run GraphEnt, helped me quite a
bit - here's
Hi Matthew,
Two anecdotes:
For one protein we had protein in pH7 with 10 mM Mn2+ and just set up
crystal trials as normal. Although at higher pH excess Mn precipitated
as MnO2, we still had Mn (2+, presumably) in the active.
For another protein, we grew apo crystals at pH8 and then gradually
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