scholarly journals A multi-model approach to assessing local and global cryo-EM map quality

2017 ◽  
Author(s):  
Mark A. Herzik ◽  
James S. Fraser ◽  
Gabriel C. Lander
Keyword(s):  
Qualitative Assessment ◽  
Model Quality ◽  
Atomic Models ◽  
Molecular Detail ◽  
Strong Indicator ◽  
Global And Local ◽  
Independent Assessment ◽  
Model Agreement ◽  
Model Approach

AbstractThere does not currently exist a standardized indicator of how well a cryo-EM-derived model represents the density from which it was generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models and to evaluate their convergence in an EM density. These analyses provide both a quantitative and qualitative assessment of the precision of the models and their representation of the density, respectively, while concurrently providing a platform for assessing both global and local EM map quality. We further use standardized datasets to provide an expected model–model agreement criterion for EM maps reported to be at 5 Å resolution or better. Associating multiple atomic models with a deposited EM map provides a rapid and accessible reporter of convergence, a strong indicator of highly resolved molecular detail, and is an important step toward an FSC-independent assessment of map and model quality.

scholarly journals Assessment of global and local model quality in CASP8 using Pcons and ProQ

2009 ◽  
Vol 77 (S9) ◽  
pp. 167-172 ◽  
Author(s):  
Per Larsson ◽  
Marcin J. Skwark ◽  
Björn Wallner ◽  
Arne Elofsson
Keyword(s):  
Local Model ◽  
Model Quality ◽  
Global And Local

scholarly journals MolProbity: all-atom structure validation for macromolecular crystallography

2009 ◽  
Vol 66 (1) ◽  
pp. 12-21 ◽  
Author(s):  
Vincent B. Chen ◽  
W. Bryan Arendall ◽  
Jeffrey J. Headd ◽  
Daniel A. Keedy ◽  
Robert M. Immormino ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Model Building ◽  
Three Dimensional ◽  
Molecular Data ◽  
Structure Validation ◽  
Model Quality ◽  
Global Database ◽  
X Ray Crystallography ◽  
Biological Interpretation ◽  
Global And Local

MolProbityis a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically inMolProbityand all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures.MolProbityis the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

SHM of Historic Damaged Churches

2013 ◽  
Vol 838-841 ◽  
pp. 2071-2078 ◽  
Author(s):  
Giosuè Boscato ◽  
Alessandra Dal Cin ◽  
Salvatore Russo ◽  
Francesca Sciarretta
Keyword(s):  
Structural Response ◽  
Modal Identification ◽  
Qualitative Assessment ◽  
The Real ◽  
Historic Monument ◽  
Characterization Of Materials ◽  
Output Only ◽  
Mechanism Of Failure ◽  
Global And Local ◽  
Residual Stiffness

The paper shows the results of monitoring activities to check the structural response and the level of damage of two historic monument of LAquila: San Pietro di Coppito and Santa Maria Paganica, that were damaged by the main earthquake of April 2009. The diagnostics operation was planned and carried out in situ and in laboratory to verify the integrity of the residual stiffness of the structures and to define the mechanical parameters of the material. The mechanical characterization of materials was carried out through destructive tests on samples, taken directly on site, and micro-destructive tests through single and double flat jacks. To give a first qualitative assessment of overall was used sonic test (non-destructive test) on the main macro-structure. The global structural health monitoring (SHM) was carried out through ambient vibrations to define the real dynamic behavior in serviceability state and to calculate - via a modal identification of output-only systems-the dynamic parameters (mode of vibration, frequencies, displacements and damping ratios). The aim of this research is to prove the reliability of different diagnostic methodologies, the real extent of global and local damage and the extent of the residual stiffness of the macro elements of the structures (façade, tower, walls of nave, transept) that are subjected to different mechanism of failure.

Sunspot Groups as Tracers of Sub-Surface Processes

2000 ◽  
Vol 179 ◽  
pp. 155-160
Author(s):  
M. H. Gokhale
Keyword(s):  
Magnetic Flux ◽  
Indian Institute ◽  
Surface Processes ◽  
The Sun ◽  
Global And Local ◽  
Sunspot Groups

AbstractData on sunspot groups have been quite useful for obtaining clues to several processes on global and local scales within the sun which lead to emergence of toroidal magnetic flux above the sun’s surface. I present here a report on such studies carried out at Indian Institute of Astrophysics during the last decade or so.

The time course of calcium deposition in shells of the barnacle (Balanus amphititre amphititre) during cyprid-juvenile metamorphosis

1994 ◽  
Vol 52 ◽  
pp. 178-179
Author(s):  
Nancy R. Wallace ◽  
Craig C. Freudenrich ◽  
Karl Wilbur ◽  
Peter Ingram ◽  
Ann LeFurgey
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Time Course ◽  
Vertical Plane ◽  
Mantle Cavity ◽  
Qualitative Assessment ◽  
Calcium Deposition ◽  
Free Swimming ◽  
Freeze Dried ◽  
Scanning Electron

The morphology of balanomorph barnacles during metamorphosis from the cyprid larval stage to the juvenile has been examined by light microscopy and scanning electron microscopy (SEM). The free-swimming cyprid attaches to a substrate, rotates 90° in the vertical plane, molts, and assumes the adult shape. The resulting metamorph is clad in soft cuticle and has an adult-like appearance with a mantle cavity, thorax with cirri, and incipient shell plates. At some time during the development from cyprid to juvenile, the barnacle begins to mineralize its shell, but it is not known whether calcification occurs before, during, or after ecdysis. To examine this issue, electron probe x-ray microanalysis (EPXMA) was used to detect calcium in cyprids and juveniles at various times during metamorphosis.Laboratory-raised, free-swimming cyprid larvae were allowed to settle on plastic coverslips in culture dishes of seawater. The cyprids were observed with a dissecting microscope, cryopreserved in liquid nitrogen-cooled liquid propane at various times (0-24 h) during metamorphosis, freeze dried, rotary carbon-coated, and examined with scanning electron microscopy (SEM). EPXMA dot maps were obtained in parallel for qualitative assessment of calcium and other elements in the carapace, wall, and opercular plates.

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