[ccp4bb] Postdoc positions available with V. Ramakrishnan

[Brown, Alan]

Posted on behalf of Venki Ramakrishnan:
The Ramakrishnan lab (http://www2.mrc-lmb.cam.ac.uk/groups/ribo/) at the 
Laboratory of Molecular Biology (LMB) is looking for up to two Postdoctoral 
Scientists to work within a programme aimed at the understanding at molecular 
level the process of protein synthesis. Full details are given here: 
goo.gl/AXzayL.
Applicants should have a PhD in structural biology (or due to complete a PhD 
within 6 months) and a strong academic record with publications in major 
journals. Experience in structural analysis of macromolecular complexes by 
crystallography or electron microscopy is required.
Please apply online: goo.gl/AXzayL.
Applications due: 28-AUG-2017

[ccp4bb] reminder that closing date for CryoEM sample preparation workshop is ***THIS SUNDAY 6th AUGUST***

[Martin Walsh]

Dear all just a reminder that our 2nd workshop aimed at newcomers to CryoEM for 
preparation and initial characterization of samples for single particle CryoEM 
experiments has a deadline for applicants of this Sunday the 6th August!!! 
…link below

http://www.diamond.ac.uk/Home/Events/2017/cryoEM-Worskhop-October-2017.html

the workshop will provide near one-to-one tuition and hands-on preparation of 
cryoem sample grids taking full advantage of the convocation of titan krios’s 
at eBIC ( http://www.diamond.ac.uk/Science/Integrated-facilities/eBIC.html )

Martin




--
Martin A. Walsh,
Diamond Light Source Ltd
Diamond House,
Harwell Science & Innovation Campus
Didcot OX11 0DE
UK
T:+44 1235 778518
E: martin.wa...@diamond.ac.uk


-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

Re: [ccp4bb] doubt regarding setting resolution cutoff

[Harry Powell]

Hi Satvik

If you're only just starting out, the first thing I would recommend is that you 
forget all about Scala! It's been effectively obsolete for 5-6 years, and any 
bugs that exist in it will not be fixed. 

It was replaced by Aimless a long time ago; Aimless is much faster than Scala 
and the scaling model is somewhat improved (what would you expect with another 
half-decade of development?).

Cutting your data at the data processing stage is probably too early in the 
structure solution process.

In your case, I'd continue analysing your structure with all your data (to 
1.861Å,) after re-scaling with Aimless ;-), then once the structure is complete 
and refined, use the "paired refinement" technique to see if the high 
resolution data are actually contributing any useful information.

HTH

Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 



On 4 Aug 2017, at 13:48, Satvik Kumar wrote:

> Dear Crystallographers,
> 
> 
> 
> I am a beginner to solving structures by x-ray crystallography. Having 
> collected a diffraction data set using laboratory source X-ray, I am now 
> processing the data. I have integrated the data successfully with the program 
> iMOSFLM using the space group P212121. 
> 
> 
> 
> During the process of scaling and merging intensities using Scala, I was 
> confronted with the question of setting the resolution cutoff. To clear the 
> doubts I had, I have read the below articles with great care:
> 
> 
> 
> 1. How good are my data and what is the resolution? Evans and Murshdov, 2013.
> 
> 2. Assessing and maximizing data quality in macromolecular crystallography. 
> Karplus and Diederichs, 2015.
> 
> 
> 
> Based on these articles it becomes very clear that I should set the 
> resolution cutoff to a value at which CC1/2 reduces to 0.2-0.4 irrespective 
> of the values of either Rmerge or I/sigI (prone to uncertainities).
> 
> 
> 
> When I ran the program Scala using high resolution cutoffs ranging from 1.861 
> A (resolution at which data was collected) to 2.33 A, I observe that at 2.0 
> A, the CC1/2 is 0.582 (outer shell) but the CC1/2 increases to 0.722 at 1.861 
> A.
> 
> 
> 
> The Karplus and Diederichs article clearly states that the CC1/2 is 1 at low 
> resolution and drops down with increasing resolution. It also states that any 
> anomaly should be carefully inspected.
> 
> 
> 
> I request the community to kindly inspect the statistics and guide me in 
> setting the optimum resolution cutoff. I have attached a pdf file containing 
> the Scala outputs (statistics and a plot of correlation coefficients versus 
> resolution) for your inspection.
> 
> 
> 
> 
> 
> Thanks,
> 
> Satvik
> 
> <040817_scala.pdf>