Biophysical Society Thematic Meeting | Trieste 2024

Emerging Theoretical Approaches to Complement Single-Particle Cryo-EM Wednesday Speaker Abstracts

MODEL-BUILDING, REFINEMENT AND VALIDATION WITH COOT Paul Emsley 1 ; 1 MRC Laboratory of Molecular Biology, Structural Studies, Cambridge, United Kingdom The interactive model-building tool, Coot, has recently has been reworked in two major ways: (i) The interface has been rebuilt practically from scratch using a new toolkit (ii) The program has been split to provide a re-usable library. The consequences of (i) are that Coot has a modern dynamic/interactive attractive GUI. Considerably more thought has been given to the layout of tools and their usability in this version than had been the case in previous versions. This version of Coot is also able to exploit multi-core processors, for validation tools such as atom overlaps, rotamer and Ramachandran plot probabilities so that they are now interactive (i.e. dynamically respond to modification of the model). The upgrade to the graphics means that informative textures are now available, density maps with large radius can be rotated with ease and Coot now uses frame-buffer techniques such as screen-space ambient occlusion and shadows.The consequences of (ii) allows (1) compilation using WebAssembly to provide the computational "back-end" of "Coot on the Web" a.k.a "Moorhen" (moorhen.org) (2) a "headless" (i.e. no-GUI) interface to Coot tools as a python module. This module can be plugged into Blender to provide structural biology tools and representations as if they were built-in."Fo-Fc-style" difference maps have been a useful tool when modifying molecular models in the light of x-ray data. This has become more useful still with the recent addition of maps that dynamically update in the light of the current model. Cryo-EM data-sets and models are considerably larger (typically) and so similar interactivity is not possible. However, we will show that, using GEMMI-based tools, something useful can be achieved. Coot is Free Software (recently it has become part of Debian GNU/Linux) and is available free of charge.https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

21