[ccp4bb] Post-doc position for SAXS at the MAX IV Laboratory
The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598Dnr=554436Type=E as well as who to contact for more information. Information about the MAX IV laboratory can be obtained at www.maxlab.lu.sehttp://www.maxlab.lu.se . best regards Marjolein Thunnissen Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.sehttp://www.mps.lu.se/ PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX
Re: [ccp4bb] Where to cut the data in this medium resolution dataset
Hi Stefan, you write The diffraction pattern looks great, the 3.4A reflections are visible by eye and the edge of the detector is about 2.8A. and for the 3.4A data Mean((I)/sd(I)) in the highest shell is 2.3 . I'm tempted to ask: what prevents you from using higher resolution data to, say, 3.2 or 3.0 A - what do you gain by throwing reflections away? Using higher resolution _will_ reduce overfitting, and should improve the model. In the presence of NCS, Rfree will be biased towards Rwork. In your case of high-order NCS, you might consider choosing the free reflections in thin shells in reciprocal space. HTH, Kay
Re: [ccp4bb] Where to cut the data in this medium resolution dataset
Hi I'd agree with Kay here - since the edge of the detector is at ~2.8Å. It is almost always worthwhile integrating to a higher resolution than you can see spots on the images - for what I would call normal datasets, I would always integrate to ~0.2Å higher (as a first estimate), then after examining scaling statistics (e.g. correlation coefficients!) decide if you can actually integrate even higher. For modern extra fine phi slicing, it's usually worthwhile integrating to an even higher resolution before making any decisions about the true resolution, especially if you have non-negligible background on the images. There are a couple of issues with integrating to *much* higher resolution than you actually have - one is due to the crystal detector refinements becoming less stable if you include too many reflections with insignificant !/sig(I) - i.e. refining against noise, and the other is in optimising the profiles measurement boxes (again, using noise to determine these will not lead to optimal values). BTW, unless you have a *really* good reason for scaling with SCALA, I would seriously consider updating your CCP4 installation and using Aimless instead. Phil Evans is no longer developing SCALA, and doesn't seem to have updated the SCALA release notes since 2010, so I suspect that any newer versions (most recent is 3.3.21) only contain minor bug fixes (but I could be wrong). On 23 Jul 2013, at 08:11, Kay Diederichs wrote: Hi Stefan, you write The diffraction pattern looks great, the 3.4A reflections are visible by eye and the edge of the detector is about 2.8A. and for the 3.4A data Mean((I)/sd(I)) in the highest shell is 2.3 . I'm tempted to ask: what prevents you from using higher resolution data to, say, 3.2 or 3.0 A - what do you gain by throwing reflections away? Using higher resolution _will_ reduce overfitting, and should improve the model. In the presence of NCS, Rfree will be biased towards Rwork. In your case of high-order NCS, you might consider choosing the free reflections in thin shells in reciprocal space. HTH, Kay The diffraction pattern looks great, the 3.4A reflections are visible by eye and the edge of the detector is about 2.8A. The crystals were 10x20x50 um in size and spacegroup is P6522. Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] IAEA- UPAT-GAEC Meeting: Second Research Coordination Meeting (RCM) on Utilization of Accelerator - Based Real - Time Methods in Investigation of Materials with High Technological Importance
ANNOUNCEMENT SECOND RESEARCH COORDINATION MEETING (RCM) ON UTILIZATION OF ACCELERATOR - BASED REAL - TIME METHODS IN INVESTIGATION OF MATERIALS WITH HIGH TECHNOLOGICAL IMPORTANCE _24-27 SEPTEMBER 2013_ WEBSITE: http://iaeaupat.wordpress.com/ [1] VENUE: Porto Rio hotel http://www.portoriohotel.gr/ [2] The Second Research Coordination Meeting (RCM) on Utilization of Accelerator - Based Real - Time Methods in Investigation of Materials with High Technological Importance, organized by the International Atomic Energy Agency (IAEA, Vienna, Austria), will be held during the period 24-27 September 2013 at the University of Patras (Patras, Greece). On behalf of the International Program Committee and the Conference organizers, we are very pleased and honored to invite you to participate to this International conference. The conference will be focused on the review of the use of accelerators for in situ real-time preparation and characterization of materials with high technological importance, including but not limited to energy production and storage. 'Real time' is defined on the scale of seconds to hours, corresponding to the events that induce changes in the sample properties. The meeting participants will be from a diverse range of accelerator-based technologies, congregating around synchrotron and particle beam users. FOR REGISTRATION PLEASE SUBMIT THE FORM (HTTP://IAEAUPAT.WORDPRESS.COM/REGISTRATION-3/ [3]), A CV (ONLY FOR STUDENTS) AND A REFERENCE LETTER (ONLY FOR STUDENTS) TILL THE 5TH OF SEPTEMBER. REGISTRATION FEE IS 150 EUROS FOR FACULTY MEMBERS AND POST DOCS AND FREE FOR STUDENTS. THE REGISTRATION FEE SHOULD BE SUBMITTED VIA BANK TRANSFER TO THE ACCOUNT: HTTP://IAEAUPAT.FILES.WORDPRESS.COM/2013/07/BANK-INFORMATION.PDF [4] IT IS ABSOLUTELY NECESSARY TO DECLARE DURING BANK TRANSFER THAT THIS AMOUNT OF MONEY SHOULD BE TRANSFERRED TO THE PROJECT: “RESEARCH COORDINATION MEETING ON UTILIZATION OF ACCELERATOR-BASED REAL- TIME METHODS IN INVESTIGATION OF MATERIALS WITH HIGH TECHNOLOGICAL IMPORTANCE 24-27 SEPTEMBER 2013″ CODE D.769 We will be glad to welcome you in Patras located in west Peloponnese in Greece. -- Irene Margiolaki Lecturer, Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, GR-26500, Patras, Greece Tel: +302610997408 Web site: http://www.biology.upatras.gr/index.php?option=com_contentview=articleid=652:2012-11-01-08-31-26catid=48Itemid=336 Links: -- [1] http://iaeaupat.wordpress.com/ [2] http://www.portoriohotel.gr/ [3] http://iaeaupat.wordpress.com/registration-3/ [4] http://iaeaupat.files.wordpress.com/2013/07/bank-information.pdf
Re: [ccp4bb] post to ccp4bb
On 7/23/13 9:01 AM, Edward A. Berry wrote: Here we need some clarification on which I/s(I) is meant - sigma(I) for the individual measurements, or sigma(I) from error propagation to the final I which as Engin notes will be lower. Isn't the reported Mean(I/sigI) in the reported Aimless table for the merged/averaged reflections (because that is what we are discussing about)? As an HKL2000 and XDS user (but not Scala/Aimless), I have definitely seen adding more images (batches) improve the reported I/sigma stats. I actually recently did a little educational experiment, where I kept on shooting, and scaling in XDS with more and more batches, to determine at which point radiation damage was defeating redundancy (in terms of I/sigI and CC1/2). Adding more batches (until a certain point) definitely increased the XSCALE-reported I/sigma stats. I thought it was the former that is to be used for selecting the cutoff, and this is somewhat confirmed by the the recent Aimless paper (ActaD 69 1204-1214 How good are my data and what is the resolution? Philip R. Evans and Garib N. Murshudov): The `maximum resolution' is estimated from the point at which I/[sigma](I) falls below 1.0 for each batch: note that this I/[sigma](I) is without averaging multiple measurements (which would not generally occur on the same image), so will be smaller than the I/[sigma] after averaging. Could it be that the reported I/sigI an average of the batch-wise I/sigI's? I would love to hear that confirmed (or denied) by the authors of Aimless. Also, why would we be using the batch-wise I/sigma's for determining resolution cutoffs? But I may be misunderstanding the point of that sentence. Engin
Re: [ccp4bb] post to ccp4bb
Hi, On Tue, Jul 23, 2013 at 10:11:04AM -0500, Engin Ozkan wrote: Isn't the reported Mean(I/sigI) in the reported Aimless table for the merged/averaged reflections (because that is what we are discussing about)? Yes - according to 1. http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Symmetry%2C_Scale%2C_Merge#Analysis_by_resolution ... the average signal/noise after averaging symmetry-related observations I/σ(I) , labelled Mn(I)/sd(Mn(I)) in the Aimless table, ... 2. section 3.2.1 of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689523/ ... from the average signal-to-noise ratio of the merged intensities as a function of resolution. ... the average intensity over symmetry mates I h is divided by its estimated error σ(I) and this ratio is averaged in resolution bins [reported as Mn(I/sd) in the program output]. So the average (denoted by and in the output) is over all unique reflections within a resolution bin - after all, those stats are reported within resolution bins. And each unique reflection is the result of (weighted) merging of all its measurements. ... as far as I understand this ... Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] post to ccp4bb
Engin Özkan wrote: Also, why would we be using the batch-wise I/sigma's for determining resolution cutoffs? Agreed. For cutoff I guess it should be the final sigma going into the refinement program that matters, irrespective of whether that was achieve by averaging more images or using a stronger dose on each image. Still I would like to here this confirmed by the experts/program authors.
Re: [ccp4bb] Where to cut the data in this medium resolution dataset
Nat, What do correct B-factors look like? What refinement strategy did you use for them? 1) If I see strong positive density in the Fo-Fc map along the backbone of two turns of an correctly placed alpha helix, therefore the B-factors are too high in that region. The model after refinement suggest less scattering in that region than is observed which is most likely explained by incorrectly high B-factors. 2) xyz, TLS and individual B-factors (no grouping). SS and ramachandran restraints on coordinates and NCS restraints on coordinates and B-factors. Note that the R-free value in the 3.4A shell is lower than the R-work (and also the Rpim in that shell!) which clearly indicates this refinement was not stable. I don't think it indicates anything about the stability of refinement - my guess would be that the NCS is biasing R-free. I suppose it could also indicate that the data in the 3.6-3.4 range are basically noise, although if the maps look better then that would suggest the opposite. I think the refinement is not parametrized correctly. Thank you, S.
