Dataset Information

Real-time PyMOL visualization for Rosetta and PyRosetta.

ABSTRACT: Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for the sole purpose of visualizing biomolecules; one of the most popular tools, PyMOL (Schrödinger), is a powerful, highly extensible, user friendly, and attractive package. Integrating Rosetta and PyMOL directly has many technical and logistical obstacles inhibiting usage. To circumvent these issues, we developed a novel solution based on transmitting biomolecular structure and energy information via UDP sockets. Rosetta and PyMOL run as separate processes, thereby avoiding many technical obstacles while visualizing information on-demand in real-time. When Rosetta detects changes in the structure of a protein, new coordinates are sent over a UDP network socket to a PyMOL instance running a UDP socket listener. PyMOL then interprets and displays the molecule. This implementation also allows remote execution of Rosetta. When combined with PyRosetta, this visualization solution provides an interactive environment for protein structure prediction and design.

SUBMITTER: Baugh EH

PROVIDER: S-EPMC3156697 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Real-time PyMOL visualization for Rosetta and PyRosetta.

Baugh Evan H EH Lyskov Sergey S Weitzner Brian D BD Gray Jeffrey J JJ

PloS one 20110816 8

Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for the sole purpose of visualizing biomolecules; one of the most popular tools, PyMOL (Schrödinger), is a ...[more]

PMID: 21857909

Similar Datasets

Project description:Mixed reality (MR) enables a novel way to visualize virtual objects on real scenarios considering physical constraints. This technology arises with other significant advances in the field of sensors fusion for human-centric 3D capturing. Recent advances for scanning the user environment, real-time visualization and 3D vision using ubiquitous systems like smartphones allow us to capture 3D data from the real world. In this paper, a disruptive application for assessing the status of indoor infrastructures is proposed. The installation and maintenance of hidden facilities such as water pipes, electrical lines and air conditioning tubes, which are usually occluded behind the wall, supposes tedious and inefficient tasks. Most of these infrastructures are digitized but they cannot be visualized onsite. In this research, we focused on the development of a new application (GEUINF) to be launched on smartphones that are capable of capturing 3D data of the real world by depth sensing. This information is relevant to determine the user position and orientation. Although previous approaches used fixed markers for this purpose, our application enables the estimation of both parameters with a centimeter accuracy without them. This novelty is possible since our method is based on a matching process between reconstructed walls of the real world and 3D planes of the replicated world in a virtual environment. Our markerless approach is based on scanning planar surfaces of the user environment and then, these are geometrically aligned with their corresponding virtual 3D entities. In a preprocessing phase, the 2D CAD geometry available from an architectural project is used to generate 3D models of an indoor building structure. In real time, these virtual elements are tracked with the real ones modeled by using ARCore library. Once the alignment between virtual and real worlds is done, the application enables the visualization, navigation and interaction with the virtual facility networks in real-time. Thus, our method may be used by private companies and public institutions responsible of the indoor facilities management and also may be integrated with other applications focused on indoor navigation.

Dataset Information

Real-time PyMOL visualization for Rosetta and PyRosetta.

Publications

Real-time PyMOL visualization for Rosetta and PyRosetta.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets