Dear all,
When you calculate the electrostatic potential surface for a protein,
what is the best way to treat
charged residues with disordered or partially ordered side-chains, e.g.
surface lysines? Do you just treat them as alanines?
Thanks,
Joe
Hi Sang Hoon,
You should do the refinement in BUSTER, which uses a novel method to
impose NCS restraints. These restraints (called LSSR restraints) were
designed specifically to provide an answer to your question in a
systematic way, by comparing the local environments of corresponding
residue
Hi Rajesh,
If you're seeing a lot of extra density coming up in the map in regions
where you previously added waters, is it possible that this extra density
corresponds to a part of your protein that you previously thought was
disordered and is thus missing from the current model? At this resolutio
> The definition game is on! :)
>
> Vectors are supposed to have direction and amplitude, unlike scalars.
I think that this is part of the problem here. Whilst vector quantities do
possess both size and direction, not everything that possesses size and
direction is necessarily a vector by definiti
Electrical current is a 4-vector, is it not?
> Correct! - and an alternating electric current is represented as a
> complex number (then it's conventional to use the symbol 'j' for
> sqrt(-1) to avoid confusion with 'i', the symbol for electric
> current!). Since as you say electric current is a
Hi,
I saw the same thing once and the cause was that the crystal had been
hideously over-exposed during data collection. As a result, essentially
all the spots at lower than 2.5A resolution were overloaded. The Wilson
plot was thus more or less flat at medium to high resolution and
accordingly the
Dear Dirk,
You are getting confused about where the sampling occurs, and this is
perhaps because we usually learn about the Shannon criterion from a
certain way around (sampling in real/time space -> periodicity of the
signal transform in frequency/reciprocal space). To see the Shannon
criterion in
> Assume you have a one dimensional crystal with a 10 Angstrom repeat.
> Someone has told you the value of the electron density at 10 equally
> spaced points in this little unit cell, but you know nothing about the
> value of the function between those points. I could spend all night
> with a
I agree with Randy Read though - it's a mistake to get too carried away
with the foul-play aspect of this. There were clearly very serious
problems with those structures anyway. What it shows is that you can
desposit just about anything in the PDB, which is quite worrying when you
consider how much
Dear BB,
We are trying to solve the structure of a complex between two proteins. We
have two crystal forms of the complex, and a partial MR solution in each.
We now want to average the density between these two forms to improve the
maps, using DMMULTI. However, there are a couple of things I don't
> Perhaps this was really my question:
>
> Do phases *necessarily* dominate a reconstruction of an entity from phases
> and amplitudes, or are we stuck in a Fourier-based world-view? (Lijun
> pointed out that the Patterson function is an example of a reconstruction
> which ignores phases, although
Dear Mona,
Yes. You can get Denzo to reject reflections on or close to ice rings, or
any other features with highly irregular background variations, by
increasing the value of the REJECT keyword (see p. 40 of the HKL2000
manual by D. Gerwith,
http://www.hkl-xray.com/hkl_web1/hkl/manual_online.pdf).
Hi Matt,
I sometimes see a similar thing with my proteins, which definitely don't
possess metal co-factors or prosthetic groups. I found that gel filtration
got rid of it - the browny-yellow stuff came out in the void fraction so I
figured it was aggregated protein. I think it was aggregation via t
Dear Richard,
I *think* it works like this, don't know if it's detailed or rigourous
enough for you!
If I(l,h,i) is the intensity of the ith observation of reflection h on
frame l, with error sig(l,h,i), and S(l) is the (inverse) scale factor to
be applied to frame l, then the error in the scaled
Dear Richard,
I *think* it works like this, don't know if it's detailed or rigourous
enough for you!
If I(l,h,i) is the intensity of the ith observation of reflection h on
frame l, with error sig(l,h,i), and S(l) is the (inverse) scale factor to
be applied to frame l, then the error in the scaled
Hi Andrew,
If there is no *protein* model built into this region of the map, then it
will be modelled by the bulk solvent correction - therefore, the negative
peaks are telling you that the mean electron density there is lower than
in the bulk solvent. Probably.
Joe
> Hello everyone I have a ques
BBSRC White Rose DTP project supervised jointly between the Cockburn,
Johnson and Ranson labs at the University of Leeds; please see
https://www.findaphd.com/phds/project/structural-and-functional-studies-on-proteins-required-for-vision/?p59606
for
more details.
- *The molecular pathogenesis of KIF5A
Hi Urmi,
When you say "antibody" you mean Fab fragments? If so, bear in mind that
Fab fragments can be quite flexible about the region inbetween the
variable and constant domains, which may be detrimental to the quality of
your crystals ... in this case, further to the advice of others on here,
you
Dear All,
A post-doctoral position is available immediately in the laboratory of Dr
Joe Cockburn, at the Astbury Centre, University of Leeds, UK to perform
structure-function studies on ciliary proteins.
The position is funded by The Wellcome Trust and is available immediately
for a period of
Dear All,
A post-doctoral position is available immediately in the laboratory of Dr
Joe Cockburn, at the Astbury Centre, University of Leeds, UK to perform
structure-function studies on ciliary transition zone proteins. The
transition zone consists of several large multi-protein complexes at the
Hello everyone,
Please see the job advert below regarding tenure-track academic fellowships
in structural molecular biology at the University of Leeds.
Cheers,
Joe
Dear All,
A number of tenure-track academic fellowships in Structural Molecular
Biology are now available at the University of
more information please visit:
https://jobs.leeds.ac.uk/Vacancy.aspx?ref=FBSMB1263
Closing date: 25th August 2023.
Kind regards,
Joe
--
Dr Joseph J B Cockburn DPhil
Program Leader, Biochemistry and Medical Biochemistry
Group Leader and Lecturer
more information please visit:
https://jobs.leeds.ac.uk/Vacancy.aspx?ref=FBSMB1263
Closing date: 2nd November 2023.
Kind regards,
Joe
--
Dr Joseph J B Cockburn DPhil
Program Leader, Biochemistry and Medical Biochemistry
Group Leader and
tails!
To apply for this role please go to:
https://jobs.leeds.ac.uk/Vacancy.aspx?ref=FBSMB1274
Deadline for applications: 05th March 2024.
Kind regards,
Joe
--
Dr Joseph J B Cockburn DPhil
Program Leader, Biochemistry and Medical Biochem
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