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Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.

59 BASIC BIOLOGICAL SCIENCES

Crater clusters and light mantle at the Apollo 17 site - A result of secondary impact from Tycho

The morphologies of Tycho secondary craters and their ejecta deposits were studied using full-moon, Lunar-Orbiter, and Apollo panoramic photographs. These data were compared with similar data for the secondary craters and light mantle of the Apollo 17 landing site. The results indicate that (1) the central crater cluster and the light mantle can be attributed to Tycho, (2) the dominant mechanism for emplacement of the light mantle was impact by secondary craters that threw material across the valley floor, and (3) level sheets of material may be emplaced locally by secondary impact. Analysis of returned samples confirms that secondary impacts rework mostly local material.

Lucchitta, B. K.

Neotectonics of Asia: Thin-shell finite-element models with faults

As India pushed into and beneath the south margin of Asia in Cenozoic time, it added a great volume of crust, which may have been (1) emplaced locally beneath Tibet, (2) distributed as regional crustal thickening of Asia, (3) converted to mantle eclogite by high-pressure metamorphism, or (4) extruded eastward to increase the area of Asia. The amount of eastward extrusion is especially controversial: plane-stress computer models of finite strain in a continuum lithosphere show minimal escape, while laboratory and theoretical plane-strain models of finite strain in a faulted lithosphere show escape as the dominant mode. We suggest computing the present (or neo)tectonics by use of the known fault network and available data on fault activity, geodesy, and stress to select the best model. We apply a new thin-shell method which can represent a faulted lithosphere of realistic rheology on a sphere, and provided predictions of present velocities, fault slip rates, and stresses for various trial rheologies and boundary conditions. To minimize artificial boundaries, the models include all of Asia east of 40 deg E and span 100 deg on the globe. The primary unknowns are the friction coefficient of faults within Asia and the amounts of shear traction applied to Asia in the Himalayan and oceanic subduction zones at its margins. Data on Quaternary fault activity prove to be most useful in rating the models. Best results are obtained with a very low fault friction of 0.085. This major heterogeneity shows that unfaulted continum models cannot be expected to give accurate simulations of the orogeny. But, even with such weak faults, only a fraction of the internal deformation is expressed as fault slip; this means that rigid microplate models cannot represent the kinematics either. A universal feature of the better models is that eastern China and southeast Asia flow rapidly eastward with respect to Siberia. The rate of escape is very sensitive to the level of shear traction in the Pacific subduction zones, which is below 6 MPa. Because this flow occurs across a wide range of latitudes, the net eastward escape is greater than the rate of crustal addition in the Himalaya. The crustal budget is balanced by extension and thinning, primarily within the Tibetan plateau and the Baikal rift. The low level of deviation stresses in the best models suggests that topographic stress plays a major role in the orogeny; thus, we have to expect that different topography in the past may have been linked with fundamentally different modes of continental collision.

Kong, Xianghong