I very much agree with Holton. I also find the following to be a simple
and very helpful argument in the discussion (it was given to me by Morten
Kjeldgaard):
"Your model should reproduce your weak data by weak Fc's - therefore you
need your weak reflections in the refinement"
I personally like
As has been suggested, you can try
other hosts - for instance Gram positive bacteria (Bacillus megaterium is an
interesting host as are other bacilli, especially if your protein is
secreted), other Gram negative bacteria (Pseudomonas for instance),
Can anyone comment on availability of Archaea e
Dear Weijun
Have a look at our REFOLD database - there are some examples of
chaperone assisted refolding as well as many protocols for refolding
of disulphide-rich proteins
http://refold.med.monash.edu.au
good luck
ashley
On 24/03/2007, at 12:23 PM, [EMAIL PROTECTED] wrote:
Hi Weijun,
Weijun,
There are literally hundreds of options you can pursue - obviously a
comprehensive and detailed list of suggestions would not fit in a little
email (in fact they don't all fit into a one-volume book).
It would be helpful to narrow things down a bit - for starters, for one or
two cases yo
I generally cut off integration at the shell wheree I/sigI < 0.5 and
then cut off merged data where MnI/sd(I) ~ 1.5. It is always easier to
to cut off data later than to re-integrate it. I never look at the
Rmerge, Rsym, Rpim or Rwhatever in the highest resolution shell. This
is because R-s
Hi Weijun,
you can get a kit from Takara (chaperone kit #3340) which has five
different chaperone plasmids (combinations of various chaperone). It
worked for me assofar that I could express huge amounts of the chaperones,
but my target protein was either not expressed at all any more (seems as
if
Dear All,
I got enclusion body in many cases when I tried to express human
proteins in E coli. I would like some suggestions on how to go about
it. I would also like to try co-expression of GroEL/GroES or
DnaJ/DnaK, and would like to know where to get the plasmids.
Any help or comments would be
Hi,
I believe such requirements concern only "Nature Methods" rather than
"Nature" by and large.
Regards,
Nadir Mrabet
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-724
UHP - Nancy 1, School of Medicine
Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Na
I thought that some of you might be interested that the journal Nature
has clarified the publication requirements regarding source code
accessibility. It is likely that some of you deserve congrats
for this. Cheers!
http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html
Although ther
Dear Colleague,
A workshop on coherent x-ray diffractive imaging in biology and
nanoscience will be held at
the 2007 APS Users Meeting. This emerging technique offers an approach
to understanding biological
systems that complements crystallography, EM, and solution x-ray
scattering by its abi
--- Juergen Bosch <[EMAIL PROTECTED]> escreveu:
> How about Coot ? Click the residue you want to
> change and hit Resdiue
> Property.
That's how I used to do it, but things start to become
boring when one needs to do it with more than one pdb
file with about 200 residues each. Does coot accept
so
Below is a horrible hack awk script which patches a file of "scores" into
a PDB file. I'm sure these a nicer way of doing this!
Phil
> Is there a program in CCP4 with a command to change
> the B-factor of a single residue? I checked the
> documentation for pdbset and it seems to assign
> B-factor
A great opportunity is on offer to work on one of the most exciting areas of
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channels and transporters.
Position Title: Postdoctoral Scientist - Membrane Receptor Signalling Group
Grade: Salary scale for Univers
Lucas Bleicher wrote:
Is there a program in CCP4 with a command to change
the B-factor of a single residue? I checked the
documentation for pdbset and it seems to assign
B-factors only for the whole molecule.
What I'd like to do is plot a given residue property
in a graphic software using the "
Is there a program in CCP4 with a command to change
the B-factor of a single residue? I checked the
documentation for pdbset and it seems to assign
B-factors only for the whole molecule.
What I'd like to do is plot a given residue property
in a graphic software using the "color by b-factor"
featur
Bart Hazes wrote:
I must admit that I've never understood the rationale for including dFc
for missing terms, although it has been discussed "lively" on a few
occassions. Yes, dFc is a better estimate for the true structure factor
than leaving out the term (equivalent to setting the amplitude
Birkbeck University of London are offering 6 scholarships in association
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I don't understand why should D be low for an incomplete shell?
According to Randy's tutorial:
D includes effects of:
difference in position or scattering factor
missing atoms
difference in overall scale or B-factor
i.e. all kinds of error in the SF model, but this is surely uncorrelated
with
Dear all,
I have anomalous data from CNS and I have converted them in CCP4 format
with 'cns2mtz' (from Kevin Cowtan). But there are F(+) and F(-) columns,
and I would like use DM which need Fmean only.
Is there an utility in CCP4 which converts F+ and F- to Fmean ?
I have tried mtzMADmod but my
Santarsiero, Bernard D. wrote:
As for the 2Fo-Fc (2mFo-DFc, or something like that) electron density map,
it again assumes that the phases are in good shape, and you essentially
lose any new information you could gain from the addition of new Fobs
terms, but the map isn't distorted since the te
I seem to recall this being discussed at some point.
For the difference electron density map, there clearly isn't a downside to
loss of reflections, i.e., the coefficients in the map generation are
formally zero for Fo-Fc (which all the scaling, weight, sigma-A bits in
there). If the phases are fa
Oops (and not object orientated programming either)
Science and Technology Facilities Council (STFC)
Charles
On 23 Mar 2007, at 11:56, Charles Ballard wrote:
Dear All,
Apologies, this is not MX related, but is important, especially if
you are an industrial user.
From the 1st April 2007,
Dear All,
Apologies, this is not MX related, but is important, especially if
you are an industrial user.
From the 1st April 2007, CCLRC will be an ex Research Council. It
is merging with PPARC and becoming Science Technologies Research
Council (STFC). CCLRC will remain a legal entity f
Qing Xie wrote:
Hi,
I'm trying to get the difference map by subtracting the native
electron density map from the complex electron density map. MAPMASK
has a function of ADD/MULT, but I don't know how to use it?
Any other ways to attack this problem in real space?
Thanks in advance,
Qing
Ye
This is a good point - I had thought that D would be very low for an
incomplete shell, but that doesnt seem to be true..
Garib - what do you think?
Eleanor
Petrus H Zwart wrote:
I typically process my data to a maximum I/sig near 1, and
completeness in
the highest resolution shell to 50% or
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