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Dear all,
i installed ccp4 6.0.2 on an amd64 machine running Ubuntu 6.10, 64bit
version. Everything is running fine except a problem i have with
truncate. At the beginning it failed giving a segmentation violation
error which i overcame using ulimit -s unlimited. Now I got another
error (quite
oh, One thing forgot to mention is that I actually collected data in
house ( about 70 frames ), the completness is high ( 98%) but the
Rmerge is high ( 0.2 ), what does this suggest?
On 4/4/07, Jenny [EMAIL PROTECTED] wrote:
Hi, All,
I got a crystal that diffracts at 3.3A in house.The crystal
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Hello,
Thanks very much to all who replied with thoughts and suggestions.
The consensus was that my interpretation was not correct, and it is not
valid to stop Refmac after TLS refinement. People also felt that the RMSD
bond/angle of 0.016/1.6 was still a little high. Phenix.refine was
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I am working with crystals with apparent I422 space group but it may be
actually I4. Twinning analysis shows twinning fraction of 0.46. I tried to
detwin the anomalous data in CCP4. Just to check the files were read and
written properly, I wrote the detwinned data in ascii. The numbers look
Hello Jenny,
0.2 Rmerge may be an indication of incorrectly assigned SG or perhaps a
misindexing by one, etc. Check what happens if you reprocess in P4.
For a 10kDa protein, your unit cell is kind of large - depending of course
on the symmetry, the higher obviusly the better. I would bet that
Streak seeding all your trays should give you a better handle on
nucleation. You might be too high in protein or precipitant w/o the
seeding, hence the showering and rare nice crystals.
Varying cryos, or cryo concentrations, or how the cryo is added can help
a lot. Try 5 or 6 different cryos at 3
The first thing to try before going down the long road of fussing
with cryo is to take a shot at room temp. and see how your crystal
diffracts in general. It is true it may be a cryo problem, but if
the non cryo protected crystals do not diffract then why would one
expect the cryo
For room temperature testing, it is much easuier to use a cryoloop
enclosed in a capillary (with some mother liqour at the top) or the
plastic tubes supplied by MiTeGen as per the method detailed in:
Skrzypczak-Jankun, E., Bianchet, M. A., Amzel, L. M. and Funk Jr., M. O.
(1996). /Acta
A small comment: crystals that do not diffract well at R.T. can still
diffract well when frozen. There are several reasons for this, including:
* poor stability of crystal once the drop is open to the air
* crystal has low tolerance for handling (capillary mount can be
challenging and cause
Dear Friends,
I have some crystals of a small RNA in sg R32 that exhibit some bizzare
behaviors and fail to give phasing solutions. I am hoping someone out there
might be able to lend some insight. All crystals come out of the same condition
and look the same morphologically but, for reasons
People also felt that the RMSD bond/angle of 0.016/1.6 was still a little
high.
This was subject of a discussion before on the board and I still don't
understand it:
If I recall correctly, even in highly accurate and precise
small molecule structures, the rmsd of corresponding
bonds and angles
Hi Dan,
In hexagonal R32 setting there is translational crystallographic
symmetry leading to systematic absences. If you think Xtal 5 is
basically the same but with slightly different packing that break the
symmetry then you will have pseudo-translational symmetry leading to one
set of very
Bernhard Rupp wrote:
People also felt that the RMSD bond/angle of 0.016/1.6 was still a little
high.
This was subject of a discussion before on the board and I still don't
understand it:
If I recall correctly, even in highly accurate and precise
small molecule structures, the rmsd of
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