Search Results for "pymol mac"
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Showing 11 open source projects for "pymol mac"
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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other... -
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SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.
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DEPRECATED - KVFinder
Cavity Detection PyMOL plugin
The KVFinder software, originally published in 2014, is deprecated. We published more recent software: parKVFinder and pyKVFinder. [parKVFinder] A Linux/macOS version is available in this GitHub repository, https://github.com/LBC-LNBio/parKVFinder, while a Windows version is in this GitHub repository, https://github.com/LBC-LNBio/parKVFinder-win. Please read and cite the original paper ParKVFinder: A thread-level parallel approach in biomolecular cavity detection... -
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PyMOL Molecular Graphics System
PyMOL is an OpenGL based molecular visualization system
The Open-Source PyMOL repository has been moved to github: https://github.com/schrodinger/pymol-open-source We still use the pymol-users mailing list here on sourceforge. Please subscribe for community support: https://pymol.org/maillist (Note: SourceForge email newsletter and special offers are optional and can be unchecked) The PyMOL community wiki has its own home: https://pymolwiki.org/ -
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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data... -
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PyInteraph
analysis of interaction networks in structural ensembles of proteins
PyInteraph is a software research tool for the analysis of structural communication protein ensembles. It has been designed to analyze MD and structural ensembles with attention to binary interactions between residues, such as hydrogen bonds, salt bridges, and hydrophobic interactions. Once the interactions have been calculated, it is able to use different classes of intra- and intermolecular interactions, combined or alone, to calculate comprehensive interaction graphs. These graphs can be... -
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Bugs
SW for HTP analysis of 3D trajectories of microorganisms
Fortran and shell-level programs originally designed for the analysis of quasi-helical trajectories of Toxoplasma gondii through Matrigel media, acquired by 3D microscopy and digitized by Imaris tracking sw, as published in [TBA]. Key sw components include a singular-value-decomposition (SVD) approach to fitting a modified Fourier series to noisy 3D coordinates measured at irregular time intervals (incorporating cross-validation for determining optimum Fourier order); correction for... -
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PreDyJE
PreDyJE is a python tool to calculate dehydrons in a protein.
PreDyJE is a python tool to calculate dehydrons in a protein PDB. Dehydrons are solvent-exposed hydrogen bonds. It runs in command-line, but a Pymol script has been developed as well. Dehydrons can be visualized in Pymol with another plugin. Structure of the program is available in the documentation. -
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PyMOL Plugins aims to provide many plugins for the PyMOL software. You can find further informations about PyMOL on this website: http://www.pymol.org/
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MIPGen
Simple Molecular Interaction Potential Generator in Python
Molecular Interaction Potential Generator MIPGEN is a python program that will calculate Molecular Interaction Potential grids over a given molecule, that could be either a protein or a small organic compound (drug). The output will be a series of grids with DX format (*.dx) that the user will be able to visualize using any Molecular visualization program like VMD, PyMol, Chimera... For more information on dependencies and usage, please read the Documentation. Users are welcome... -
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--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.
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