University of Wisconsin–Madison

Tutorial Materials – Molecular Graphics

Tutorials are organized by software.

Access these pages either with the menu at right, or by browsing below.

Each page will provide tutorial materials in various formats.

CRISPR RNA-guided surveillnace complex, Cascade, bound to a ssDNA target. (PDB ID 4QYZ)

PyMOL

The material for this series of workshops is provided as a printed workbook of 173 pages loaned during classes. PyMOL workshops are currently split into 3 successive sessions.

A molecule computationally docked. ChimeraX image by JYS.

Autodock

AutoDock is a molecular modeling simulation software designed for protein-ligand docking, a techinique to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme. AutoDock Vina is an improved version has an improved local search routine that makes use of multicore/multi-CPU computer setups. AutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude. …

Human deoxyhemoglobin (PDB ID 2HHB)

Chimera

Background UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

Cover of Sybyl 2.1 installation manual.

Sybyl

Guest speaker: Dr. Kenneth Satyshur Profiles: UW Small molecule screening facility LinkedIn Research Gate Background Sybyl is a general molecular modeling program that consists of a number of computational chemistry modules to describe and predict molecular behaviour. by Tripos, now a subsidiary of Cetara, Inc.. The program suite SYBYL The Basic module performs the task of reading or sketching structures and initiating minimisations…

Oxymyoglobin - Physeter catodon (sperm whale)- (PDB ID 1MBO)

ChimeraX

Background UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

Homology modeling process.

MODELLER

What is MODELLER? MODELLER is most frequently used for homology modeling of protein structure by satisfaction of spatial restraints 1: The user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate a model with all non-hydrogen atoms.