Some software tips and tricks useful for IM data manipulation/analysis/visualisation
OMICtools, a community platform to find bioinformatics tools
Description OMICtools is a manually curated web resource to retrieve and discuss biological data analysis analysis tools. This goes from standalone software to APIs and databases. All the tools are classified either as Technologies (Mass spectrometry, NMR spectroscopy, BioImaging, etc.) or Interpretation (Proteomics & Metabolomics, Systems & Synthetic biology, etc.).The different filters allow you to refine your search […]
Read MoreChimeraX, a new version of Chimera available on SBgrid
Introduction UCSF Chimera is one of the most popular molecular viewer. It is currently developed by the Resource for Biocomputing, Visualization, and Informatics at University of California, San Francisco. Among its many features, Chimera is probably the best software for the interactive visualisation and analysis density maps. It allows for a fine-tuning of the density maps and […]
Read MoreRun GROMACS within PyMol with Dynamics
Introduction GROMACS is a well-known and broadly used suite for molecular dynamics simulations. It is a free, open-source software that supports several force-fields (GROMOS, AMBER, CHARM, etc …) and is one of the flagship software within BioExcel. PyMol is a popular 3D molecular visualization system, maintained and distributed by Schrödinger on an open-source foundation. It […]
Read MoreParse and manipulate PDB files with shell and PyMol
Many tasks we are performing in Integrative Modelling involve 3D structures of molecules. Visualising them, modifying them to fit a particular program requirements or just parsing them to analyse them can sometimes be time-consuming. We are presenting here two approaches to quickly and easily manipulate PDB files. Shell scripting (based on PDB-tools suite) Several short and efficient python […]
Read More