Dear Hailiang,
This apparently is not the real physics, since the
electron density has to be positive everywhere (hope I am right).
Yes, you are right when you are talking about the electron density.
You are wrong when you are talking about a Fourier synthesis calculated
always at a finite r
Or you could just bug me to find the PNGaseF expression plasmid that I should
have in the freezer somewhere!
LOO T., PATCHETT M. L., NORRIS G. E. & LOTT J. S. “Using Secretion to Solve a
Solubility Problem: High-yield Expression in E. coli and Purification of the
Bacterial Glycoamidase PNGase F
The question of what textbook to use is very much context sensitive, that
is,
it depends on what the reader wants and needs to know. Unfortunately, this
question us easy to answer with hindsight, but not so obvious to the person
looking for answers.
Having said that, I declare a conflict of intere
Edward A. Berry wrote:
Hailiang Zhang wrote:
Hi there:
I found that the grid values in the map file generated by CCP4-fft
generally has a mean value of ~0, and of course there will be lots of
negative values. This apparently is not the real physics, since the
electron density has to be positive
Hailiang Zhang wrote:
Hi there:
I found that the grid values in the map file generated by CCP4-fft
generally has a mean value of ~0, and of course there will be lots of
negative values. This apparently is not the real physics, since the
electron density has to be positive everywhere (hope I am r
Back when I was a graduate student, my favorite book was Drenth.
However, that book was never a favorite with most students, who
preferred Crystallography Made Crystal Clear. I also think the Blow
book is good. I'm not familiar with the newer books written by our
mailing list colleagues.
ho
Hi there:
I found that the grid values in the map file generated by CCP4-fft
generally has a mean value of ~0, and of course there will be lots of
negative values. This apparently is not the real physics, since the
electron density has to be positive everywhere (hope I am right). Can
somebody give
Fellow CCPers,
Slightly off-topic question: I recently produced several large batches of
B834 auxotrophic E. coli cells in minimal media to make
selenomethionine-labeled protein. While growing, the cells had a slightly
pink color to them. After cell lysis and centrifugation at 12,000xg, a
brigh
Hi folks
This should not be confused with the IUCr's Commission on
Crystallographic Computing Newsletters which have been produced at
least annually since 2003, and which are aimed at crystallographers
rather than only at structural biologists.
On 8 Jul 2010, at 21:33, Paul Adams wrote:
Dear Colleagues,
I am pleased to announce the publication of the first issue of the
Computational Crystallography Newsletter:
http://www.phenix-online.org/newsletter/
It features articles, meeting announcements and reports,
information on research and other items of interest t
I like David Blow's book for beginners -- one can get the gist of things
without having much math:
http://www.abebooks.com/servlet/SearchResults?an=blow&sts=t&tn=crystallography&x=35&y=6
Bernhard Rupp's book, mentioned earlier, is the current gold standard, in
my view.
Bob
On Thu, 8 Jul 2010
Having recently completed the CSHL Macromolecular crystallography course, I can
recommend Introduction to Macromolecular Crystallography by Alexander McPherson
(ISBN 987-0-470-18590-2). I am posting the link below:
http://www.amazon.com/Introduction-Macromolecular-Crystallography-Alexander-McPhe
Hi Peter,
I understood your situation and I believe the best literature for you is the
Dr. Rupp's Book:
"Biomolecular Crystallography: Principles, Practice, and Application to
Structural Biology"
Author: Benhard Rupp.
Good luck in your studies.
Best regards,
Júlio César
-Mensagem o
At the risk of appearing immodest:
http://www.amazon.com/Protein-Crystallography-Eaton-E-Lattman/dp/0801888069/ref=sr_1_10?ie=UTF8&s=books&qid=1278618335&sr=1-10
On 8 Jul 2010, at 3:35 PM, Peter Hsu wrote:
> Hi all,
>
> I haven't gotten past the phase of growing the crystal, but I'd certainly
This book worked great for me:
http://www.amazon.com/Crystallography-Made-Crystal-Clear-Third/dp/0125870736/ref=sr_1_3?ie=UTF8&s=books&qid=1278618216&sr=1-3
Cheers,
Thomas
On Thu, Jul 8, 2010 at 12:35, Peter Hsu wrote:
> Hi all,
>
> I haven't gotten past the phase of growing the crystal, but I'
Hi all,
I haven't gotten past the phase of growing the crystal, but I'd certainly still
like to learn the actual theories of crystallography. Can anyone recommend a
good beginner to mid-level text on macromolecular crystallography?
Thanks,
Peter
On Thursday 08 July 2010 11:03:30 am Parthasarathy Sampathkumar wrote:
> Dear All,
>
> Back ground:
> This is my first experience with a twined dataset. Crystals belong to a
> small domain of 132 aa, out of which ~40 residues appears to be disordered
> (~30 of those from C-terminal and C-term His6
Hi Partha -
A few thoughts:
1. If you attach logs, at least gzip them ...
2. From the fact that Rfree goes down when twinning is switched off, I
would think there is no twining.
3. The intensity distribution (moment of E, etc) suggest no twining.
The twining operator you use is the crystallo
There is a postdoctoral position in Structural Biology available at the
Pfizer site in Cambridge, Massachusetts. The project involves solving
the structures of related signalling protein/receptor complexes and then
using computational modeling to design new molecules with enhanced
specificity. We
Sampath
With regard to your question on what sort of statistics you should get
within
structure determination you might find this service at the PDBe useful :
http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp
You can view and manipulate distributions of R, Rfree and R-Rfree along
mapmask will do this.
Eleanor
See the documentation - it is a bit confalued but certainly works..
Hailiang Zhang wrote:
Hi,
I want to calculate the portion of the "noise" density with respect to the
whole unit cell (assuming the model is good enough). I plan to first
calculate the integral den
Hi,
In idiffdisp (v. 6.1.13 and I presume also in earlier versions), if I read in
a bunch of images as a sector, the function 'two clicks to define a line' is
not working (it's not lit in fact). This function is quite useful for looking
into difficult cases e.g. where weak reflections are igno
Something else to consider is what is your space group ?
P212121 but truly P21 with twinning fraction close to 0.5 ?
That's one of my recent cases. 1.9 Å data beautifully refined & built but the
Rwork/Rfree gap was 13 percent. After changing the space group and applying the
twin law the gap is 3
"badly built model" reminds me of another possible reason:
if you have an old version of ccp4 installed (before 6.1??), there is a default
weight of 0.3 for refmac between data and restraints.
This value is - in my experience - way too high for "normal" resolution and at
the beginning of refinemen
I do agree with Tim's reasoning in general, but as Pavel also implied
by offering the statistics,
I would not be worried about the difference, but by the unreasonably
high absolute value of Free R for 2.0 A resolution.
I do not think that its simple 'over-fitting' and my worry would not
be
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