Fitting molecular fragments into electron density

A number of techniques for the location of small and medium-sized model fragments in experimentally phased electron-density maps are explored. The application of one of these techniques to automated model building is discussed

Comment on ''the impact of recent forcing and ocean heat uptake data on estimates of climate sensitivity''

In 2018, Lewis and Curry presented a method for estimating the transient climate response (TCR) of the climate system from the temperature change between two time windows: an early baseline period in the nineteenth century and a modern period primarily in the twenty-first century. The results suggest a lower value of TCR than estimates from climate model simulations. Previous studies have identified uncertainty in the historical forcings, the impact of the time evolution of the forcing on temperature response, and observational issues as contributory factors to this disagreement. We investigate a further factor: uncertainty in the bias corrections applied to historical sea surface temperature data. This uncertainty can particularly affect the estimation of variables on decadal time scales and therefore affect the estimation of TCR using the window method as well as estimates of internal variability. We demonstrate that use of the whole historical record can mitigate the impacts of working with short time windows to some extent, particularly with respect to the early part of the record

Recent developments in classical density modification

Several new methods are evaluated for use in the improvement of experimental phases in the framework of a classical density-modification calculation. These methods have been implemented in a new computer program, Parrot

Completion of autobuilt protein models using a database of protein fragments

Two developments in the process of automated protein model building in the Buccaneer software are described: the use of a database of protein fragments in improving the model completeness and the assembly of disconnected chain fragments into complete molecules

Automated nucleic acid chain tracing in real time

The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the `fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into the Coot software package

From crystal to structure with CCP4

An introduction to the proceedings of the CCP4 study weekend is given

Pacific variability reconciles observed and modelled global mean temperature increase since 1950

Global mean temperature change simulated by climate models deviates from the observed temperature increase during decadal-scale periods in the past. In particular, warming during the ‘global warming hiatus’ in the early twenty-first century appears overestimated in CMIP5 and CMIP6 multi-model means. We examine the role of equatorial Pacific variability in these divergences since 1950 by comparing 18 studies that quantify the Pacific contribution to the ‘hiatus’ and earlier periods and by investigating the reasons for differing results. During the ‘global warming hiatus’ from 1992 to 2012, the estimated contributions differ by a factor of five, with multiple linear regression approaches generally indicating a smaller contribution of Pacific variability to global temperature than climate model experiments where the simulated tropical Pacific sea surface temperature (SST) or wind stress anomalies are nudged towards observations. These so-called pacemaker experiments suggest that the ‘hiatus’ is fully explained and possibly over-explained by Pacific variability. Most of the spread across the studies can be attributed to two factors: neglecting the forced signal in tropical Pacific SST, which is often the case in multiple regression studies but not in pacemaker experiments, underestimates the Pacific contribution to global temperature change by a factor of two during the ‘hiatus’; the sensitivity with which the global temperature responds to Pacific variability varies by a factor of two between models on a decadal time scale, questioning the robustness of single model pacemaker experiments. Once we have accounted for these factors, the CMIP5 mean warming adjusted for Pacific variability reproduces the observed annual global mean temperature closely, with a correlation coefficient of 0.985 from 1950 to 2018. The CMIP6 ensemble performs less favourably but improves if the models with the highest transient climate response are omitted from the ensemble mean

Evaluating the impact of U.S. Historical Climatology Network homogenization using the U.S. Climate Reference Network

Numerous inhomogeneities including station moves, instrument changes, and time of observation changes in the U.S. Historical Climatological Network (USHCN) complicate the assessment of long-term temperature trends. Detection and correction of inhomogeneities in raw temperature records have been undertaken by NOAA and other groups using automated pairwise neighbor comparison approaches, but these have proven controversial due to the large trend impact of homogenization in the United States. The new U.S. Climate Reference Network (USCRN) provides a homogenous set of surface temperature observations that can serve as an effective empirical test of adjustments to raw USHCN stations. By comparing nearby pairs of USHCN and USCRN stations, we find that adjustments make both trends and monthly anomalies from USHCN stations much more similar to those of neighboring USCRN stations for the period from 2004 to 2015 when the networks overlap. These results improve our confidence in the reliability of homogenized surface temperature records

Coverage bias in the HadCRUT4 temperature series and its impact on recent temperature trends

Incomplete global coverage is a potential source of bias in global temperature reconstructions if the unsampled regions are not uniformly distributed over the planet's surface. The widely used Hadley Centre-Climatic Reseach Unit Version 4 (HadCRUT4) dataset covers on average about 84% of the globe over recent decades, with the unsampled regions being concentrated at the poles and over Africa. Three existing reconstructions with near-global coverage are examined, each suggesting that HadCRUT4 is subject to bias due to its treatment of unobserved regions. Two alternative approaches for reconstructing global temperatures are explored, one based on an optimal interpolation algorithm and the other a hybrid method incorporating additional information from the satellite temperature record. The methods are validated on the basis of their skill at reconstructing omitted sets of observations. Both methods provide results superior to excluding the unsampled regions, with the hybrid method showing particular skill around the regions where no observations are available. Temperature trends are compared for the hybrid global temperature reconstruction and the raw HadCRUT4 data. The widely quoted trend since 1997 in the hybrid global reconstruction is two and a half times greater than the corresponding trend in the coverage-biased HadCRUT4 data. Coverage bias causes a cool bias in recent temperatures relative to the late 1990s, which increases from around 1998 to the present. Trends starting in 1997 or 1998 are particularly biased with respect to the global trend. The issue is exacerbated by the strong El Niño event of 1997-1998, which also tends to suppress trends starting during those years