So, a bit like Fold-it but with actual data? :-D
Dr David C Briggs PhD
http://about.me/david_briggs
On 16 May 2014 06:19, Pavel Afonine pafon...@gmail.com wrote:
What about structures that are obviously wrong based on inspection of the
density, but no one has bothered to challenge yet? The
Dear Matt,
95% solvent is highly unlikely, but not impossible. Did you have a look at the
crystal packing? Are there continuous crystal contacts in all three dimensions,
or are there layers of molecules that are not connected? Are you sure your
space group is P212121 and not one of the other
I am also in favor of two versions of the pdb: one archive version with all
models as originally deposited including retracted and corrected versions,
which are useful for educational purposes, and a curated version with only
models that meet a minimum of validation criteria, including credible
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Dear Hongshi,
if the numbers do not vary too much, e.g. between 0.2 and 0.6, I would
deposit the calculated mean. I would say that the reported mosaicity
is not too important a figure for a publication. It is interesting
when it comes to data
Hi
I'm sure that a real HKL or Denzo/Scalepack expert will correct me, but my
recollection is that you don't use any of the values from Denzo, but the value
from Scalepack (see
http://www.hkl-xray.com/sites/default/files/HKL2000manual/chapter3/step14-1.htm,
for example).
On 16 May 2014, at
Hi ccp4bb
Two postdoctoral positions in X-ray crystallography/drug discovery are
currently available at University College London/Magnus Life Science.
Please see link for further details.
http://www.magnuslifescience.co.uk/careers/
Best
2014-05-15 9:53 GMT-03:00 Colin Nave colin.n...@diamond.ac.uk:
Of course exponential growth can’t go on forever – the hidden point behind
my question.
A nice example from another biological database is Swissprot. It had an
exponential-like growth until 2009, and now it's somewhat linear:
16-May-2014
Dear Patrick,
Proteopedia [http://proteopedia.org] uses exactly the same style for
referencing published material.
Proteopedia allows for the easy insertion of Pubmed and DOI references by only
requesting from the user to enter the Pubmed or DOI ids. We have extended the
same
Matt,
In addition to the suggestions of the others, have you done a simple self
rotation function? It can tell you quite a bit about how things are packed and
give you strict criteria for choosing one solution over another. As Roger
said, choosing an even number of monomers in the ASU is a
Hello,
for convenience I might ask the CCP4BB: does anyone know what the status of
the PDB is with regard to the storage of diffraction images? I had the
impression that this matter had been discussed as far back as ~15 years ago
but what came out of it?
Short of storing images, which is the
On Fri, May 16, 2014 at 7:12 AM, esse...@helix.nih.gov wrote:
Short of storing images, which is the ultimate preservation of primary
information, I have always been puzzled by the fact that the PDB only
stores
unique reflections i.e. no Friedel pairs even when provided. Is this
outdated
Dear All,
Recently we collected some data of a MBP fusion protein, at around 4A
resolution. The protein itself is about half of the MBP size. However when
we tried to solve it with MR, it failed. We tried to use MBP alone,
homology model of target protein alone, and MBP+model. It is very strange
Hi Nat,
okay. Looks like I missed this. Perhaps the data sets that I wish had Fiedel
pairs didn't and this solidified my incorrect assumption(s) about pdb
policy.
So Fiedel pairs are there when deposited. What about storage of images? Is it
coming soon - it feels like that it is about time
Hi Joel and Jaime - very nice to hear from you. I hope everything is going
well in Rehovot.
Proteopedia is the natural place to put comments etc. However it might
look more natural if there was more info there in the first place - ie if
people gave more explanation about the significance of
Hi Niu,
Several things come to mind. First, it may not be trivial when the first
component to be placed is ~20kDa and the second component (SU) is ~43kDa.
The signal after placing the first component may be weak. Also, if the
model for the smaller SU has low sequence identity with the target and
Dear Niu,
When it works, crystallising a fusion protein can be great, with the big
advantage that placing a model for the (known) carrier protein gives free phase
information. Certainly there are examples of this working, but in the early
days of this (20 years or so ago?), I remember hearing
Dear all,
Thanks for all your reply and useful comment on this.
Harry,
You are right. I think there are individual mosaicity value corresponding
to each image from scalepack. Clearly, we can get either average or range
for report.
best,
Hongshi
On Fri, May 16, 2014 at 2:26 AM, Harry Powell
If you refine crystal mosaicity (I assume there is a way to do that in the
gui)
then scalepack prints out a single value for the crystal (search the logfile
for mosaicity)
eab
On 05/16/2014 12:07 PM, hongshi WANG wrote:
Dear all,
Thanks for all your reply and useful comment on this.
Harry,
HKL-2000 has a menu button at the top Report. If you click on that a report
is generated with mosaicity range explicitly listed.
It is probably not suitable to describe a crystal as having a single mosaicity
value because mosaicity may be anisotropic. It should be obvious that a unit
cell
Dear Randy,
Over the last ~6 years, we have tried to use the MBP tag to enhance
crystallization on 10 proteins. Only one that couldn't crystallize by
itself in the end crystallized with the fusion tag. However,
unfortunately, the target protein (~10 kDa) turned out to be in the big
cavity of the
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