[ccp4bb] Post doc position at the Astbury Centre, University of Leeds, UK

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

[ccp4bb] Structural biology postdoc position at Astbury Centre, University of Leeds

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

[ccp4bb] 3 year postdoctoral position at the University of Leeds

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

[ccp4bb] PhD positions in structural biology at the Astbury Centre, University of Leeds

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

[ccp4bb] tenure-track academic fellowships in structural molecular biology at the University of Leeds

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

[ccp4bb] Post-doctoral position at the Astbury Centre, Leeds, UK

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

[ccp4bb] Post-doctoral position in Structural Biology of Cilia, Astbury Centre, Leeds, UK

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

Re: [ccp4bb] Improve diffraction ...any ideas?

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

Re: [ccp4bb] sudden drop in R/Rfree

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

Re: [ccp4bb] Lattice sampling and resolution - a seeming paradox?

> 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

Re: [ccp4bb] Lattice sampling and resolution - a seeming paradox?

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

Re: [ccp4bb] Bfactor is zero?

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

Re: [ccp4bb] vector and scalars

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

Re: [ccp4bb] vector and scalars

> 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

Re: [ccp4bb] Why Do Phases Dominate?

> 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

[ccp4bb] DMMULTI question

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

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures

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

Re: [ccp4bb] negative density peaks where there is no model.

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

Re: [ccp4bb] Scalepack error model?

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

Re: [ccp4bb] Scalepack error model?

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

Re: [ccp4bb] two identical proteins in one asymmetric unit

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

[ccp4bb] Partially ordered side-chains and electrostatics

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

Re: [ccp4bb] Protein Color

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

Re: [ccp4bb] Question re: ice rings in diffraction data

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).