The cycles of accretion, nuclear interconversions and cooling of matter is far
from complete but if we fast forward the universe by n billions of years, it's
remarkable how much of it turns out to be crystalline. A bit like a
crystallization trial at a cosmic scale. Does assume an
Hi all,
There are so many software for MR, such as phaser, balbe,molrep, and amore.
What is difference between them? Which one is powerful?
Please give some comments for these software?Thank you.
Sincerely,
lisa
Hi Lisa,
I would start with learning AMoRe. It is relatively simple, runs fast and uses
little memory, so you can experiment easily with lots of parameters. It is also
relatively easy to modify the parameters, radii etc. and get a feel for which
ones to use. If after a few days or weeks you
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Dear James,
my guess is that xprep removes ( 0 0 0) for a better contrast, but I
don't know for sure - George is going to tell you, I guess, because he
will know ;-)
The reason I answer is rather a comment: I would not call the tutorial
you refer to
There are three general approaches to molecular replacement:
1. rotation-translation algorithms: these divide the 6-dimensional
problem of placing a replacement model in the ASU into two
sequential 3-parameter searches, which, if it works, converges more
quickly than a 6-dimensional
Older members of the bulletin board will be sad to learn that Struther Arnott
FRS, fibre diffractionist and biophysicist (as well as former St Andrews
Principal) died on Saturday.
Jim Naismith
James H. Naismith FRSE FMedSci| naism...@st-andrews.ac.uk
Professor of Chemical Biology
Sad news indeed, he mentored my mentors, His influence on crystallography
(rather than fibre diffraction) in not always as well appreciated as it
might be.
Peter
On 22 April 2013 14:44, James Naismith naism...@st-andrews.ac.uk wrote:
Older members of the bulletin board will be sad to learn
Does anyone have a nice graphic of type X collagen?
Thanks in advance.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Hi all, perhaps not the right forum but...
...is there a way in coot to make a lysine side-chain // carboxy-terminal
iso-peptide bond?
Cheers in advance
Dean
Dear All,
I am presently faced with a peculiar case in the lab. We are expressing a
protein in E. coli and we are able to express it as a fusion
protein without problems . Fusion cleavage goes well and the final product
looks homogenous by size-exclusion chromatography with the expected
molecular
reminds me of structure 1NEU, although here the gelation was reversible, see
ref and abstract below - the paper has a photo of a tube of soluble protein and
gelled protein
we have also had a couple of cold-sensitive proteins in our hands, that
precipitated at 4 degrees when concentrated, but
Dear Wenzong,
Could you provide a bit more details please? Do you simply require some
visualisation tool e.g. pymol to superimpose your turn mimic on your
protein/peptide structure or are you looking for more indepth modelling to say
identify new scaffolds to build amino acid sidechains onto
I want to build the loop based on a computer screen against my peptide.
Thanks
Wenzong
- Original Message -
From: Joel Tyndall joel.tynd...@otago.ac.nz
To: Wenzong Li wenzong...@cm.utexas.edu, CCP4BB@JISCMAIL.AC.UK
Sent: Monday, April 22, 2013 6:10:09 PM
Subject: RE: [ccp4bb] Modelling
Does your protein have multiple exposed Cys residues? I have observed this
before with a protein I worked with that had many exposed Cys residues. In my
case I could add more DTT and minutes later the gel would be completely
dissipated. My hand-wavy explanation was that the protein stays folded
I have experienced a similar thing with lysozyme immediately forming a clear
gel when attempting to dissolve at high concentration in D2O. The clear gel
did not readily dissolve on dilution (in D2O) and I discarded it. I later made
the sample by dissolving in H2O and dialysing to D2O.
Thanks to All for the diligent answers to my query,
The protein is not thermophilic and has only one cysteine. We are working
in presence of freshly added reducing agent and glycerol to promote
solubility (well kinda it seems).
This is not an RNA or DNA binding protein and it has no
Wenzong,
You may want to look at rosetta's design modules.
Pete
Wenzong Li wrote:
I want to build the loop based on a computer screen against my peptide.
Thanks
Wenzong
- Original Message -
From: Joel Tyndall joel.tynd...@otago.ac.nz
To: Wenzong Li wenzong...@cm.utexas.edu,
Hi Pascal,
Your problem brings to mind this paper:
FG-Rich Repeats of Nuclear Pore Proteins Form a Three-Dimensional Meshwork
with Hydrogel-Like Properties Science 3 November 2006: 314 (5800), 815-817.[DOI:
10.1126/science.1132516]
Of course, in that case, the gellation was deliberate, but
Ahh Ok, now I see. I guess you need a search engine that idenitifies an
antiparallel beta sheet with a turn. Whilst I don't know how to do it, maybe
the pdb or epdb may do this or even modeller loop via accelrys interface
Joel
-Original Message-
From: CCP4 bulletin board
Hi all -
I am looking for examples of structures of protein-protein complexes
(homo or hetero) wherein the crystallized proteins had mutations
within their binding interfaces, and yet the same (weakened)
interactions were still recapitulated in crystal contacts.
Any leads would be much
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