SeeSAR 7.1 Beginners Guide. June 2017

Size: px
Start display at page:

Download "SeeSAR 7.1 Beginners Guide. June 2017"

Transcription

1 SeeSAR 7.1 Beginners Guide June 2017

2 Part 1: Basics 1

3 Type a pdb code and press return or Load your own protein or already existing project, or Just load molecules To begin, let s type 2zff and download it from the pdb! 2

4 The protein is loaded and protein ligands are listed in the table all fully automatic. Table - drag right rim to re-size - click entries to select Select a protein in the table on top to see the bound ligands. Optionally unfold some protein information here. 3D-viewer: - right-click to rotate - mouse-wheel to zoom - middle-click to shift 3

5 If you want to customize the layout of SeeSAR, click on the appearance button in the top right toolbar. Adjust background color Change the table layout Switch between dark and light theme Adjust label size Switch to color blindness mode For this guide everything stays on default, but please feel free to change it! 4

6 Note that there are two tabs. In the proteins tab you find all proteins and bound ligands. Note that each of these has it s own binding site (click on a ligand to see it in atomic detail). The molecules tab is to further work with any set of molecules in a common binding site. To transfer a protein ligand to the molecules table click on the menu button first and the molecule copy button second. 5

7 Note: working with the molecules table requires the definition of a common binding site. To do so, click on the define binding site button. 6

8 The define binding site dialog opens replacing the main menu! 1. Select a protein for binding site definition from the drop-down menu. 2. Use/select a molecule from the table to define the binding site or determine unoccupied pockets. For now, let s do the former and leave the dialog. 3. Upon selection the binding site appears in pink in the 3D window. Now leave the dialog via the green exit button and confirm your choice of binding site with the checkmark! Note: this brings you back to the main menu 7

9 The molecules table offers a lot of options: - on top you find general functions with an effect on multiple molecules in the table which you can select with the checkbox in the first column. - the selected molecule provides further functions (accessible through its menu button) To estimate the binding affinity click the thumbs-up button! Next, let s inspect the binding mode in detail. Zoom in using the space key on the keyboard! 8

10 As the 3D view easily gets busy, let s customize the visualization. 9

11 The view controls let you toggle on/off: Protein components Torsion coloring Surface Hyde coronas Unoccupied space Binding Site A click on the button toggles the visibility. Via the small triangles you may access more options. Let s hide the secondary structure, ligands, and metal ions as shown! Note: a click on the checkmark toggles the visibility of individual components. Clicking on header toggles the visibility of all components in the column/row (useful with several proteins). 10

12 The colored coronas depict the contributions of each atom to the estimated binding affinity. Red means unfavorable contribution, green a favorable contribution and the bigger the sphere is, the stronger is the effect. No sphere means that such atom is not estimated to have a significant impact on the binding affinity. To access the moleculespecific functions now, click on the menu button! 11

13 For a selected molecule you can: select mark as favorite annotate calculate affinity generate poses edit ligand delete toggle permanent visibility We want to edit the molecule so click on the edit button! This will open the editor menu at the top, again replacing the main menu. 12

14 The editor-menu lets you: add atoms or rings change charge adjust torsion remove atoms store the current molecule to the table change atom type change bond type ReCore parts of molecule undo/ redo exit the editor To edit a molecule ALWAYS: 1. select (atoms or bonds) 2. modify (using the function of choice from above) Note that many editor functions have shortcut-keys. E.g. select a bond and type 1, 2 or, 3 on the keyboard, or select an atom and type the element (C, N, O, ). 13

15 As an exercise, we add an amino group to the ring by selecting the Hydrogen in meta-position and changing its element type to N. Note: during editing you see all Hydrogens but no estimated affinity and no coronas. To see them, 1 st add the edited ligand to the table (with or without generation of poses), 2 nd select the new entry in the table and 3 rd calculate the affinity with the thumbs-up button! 14

16 If you click on the molecule entry you see the estimated affinity and related coronas, but only polar Hydrogens. The editor menu is locked now. To continue editing, click on the Resume button on top! 15

17 Now lets add a methyl group to the 5-membered ring. Again storing this in the table, we see a further increased affinity estimate. Let s leave the editor now by clicking on the exit button, keeping all edits with the checkmark. 16

18 At the top of the molecule table, you find the following options that act on multiple molecules in the table: define new binding site generate poses save molecules permanent visibility send to StarDrop toggle table/ grid view optimize & calculate Hyde edit molecules delete molecules filter molecules Hyde performance assessment 17

19 For report-preparation, you find the option to take a screenshot under the utilities button in the upper right toolbar: center view take screenshot For binding mode analysis, you find some useful mouse modes under the next button to the right: add labels measure distances measure angle measure torsion delete labels 18

20 Part 2: Adding own molecules 19

21 If you want to add your own molecules to a SeeSAR-session: use e.g. your favorite drawing tool and save the molecules as sdf-, smiles-, or mol2-file. Then load them in SeeSAR. In the source column you see where a molecule came from. 20

22 Loaded molecules may not yet be placed in the binding site (the information icon tells you upon mouse-over). In such case, select the molecules and use the Generate Poses button! (Note: obviously you can skip this step if your molecules are already placed in the binding site, e.g. by an external docking). 21

23 At most 10 poses per molecule are generate this way. To get the estimated affinities, press the thumbs-up button at the top of the table! Note: you may restrict the Hyde-calculation to a pre-selected set of checked molecules. 22

24 1 2 Now the estimated affinities appear as a range on the logarithmic (!) scale. To inspect multiple poses in comparison, toggle the permanent visibility with a click on the eye button (1.). Now it will appear in purple color and stay visible as you select other molecules. You can add more physico-chemical and ADME-properties as well as pharmacological parameters to your table with a click on the table button (2.). 23

25 By now you have a lot of interesting values and possibly many molecules. You may want to apply some filters Clicking on the filter button at the top opens the filter panel on the right side of the table. 24

26 To add a filter, select/determine a property from the dropdown list and push the Apply filters button (or simply hit return). For a better overview, slide the last filter element to the on position and see (from all those passing the filters) only the best-scoring pose per molecule. To hide the filter dialog push the filter button again. Note that filters may still be active then! 25

27 Part 3: Adding more proteins 26

28 Let s load in addition 2zda from the PDB. 27

29 Now you have 2 proteins in the protein table. As before, the protein ligands of the selected protein are listed underneath. In the binding site you see now the amino acids from both proteins. The selected protein appears a little brighter. To better discriminate between the proteins let s change the color in the protein table 28

30 This protein was used to determine the common binding site. To select a custom color, click on the rectangle in the second column! Different proteinrelated functions are accessible via the menu button. You may reset it with a click in the x. 29

31 Open the visualization dialog and toggle the visibility (of ribbons, binding site, ligands, water, and metals) for all (with a click on the column/row header) or individual components! 30

32 This has been a lot At any time find help within SeeSAR here! 31

33 Now we wish you happy SeeSAR-ing! 32

Ligand Scout Tutorials

Ligand Scout Tutorials Ligand Scout Tutorials Step : Creating a pharmacophore from a protein-ligand complex. Type ke6 in the upper right area of the screen and press the button Download *+. The protein will be downloaded and

More information

Tutorial. Getting started. Sample to Insight. March 31, 2016

Tutorial. Getting started. Sample to Insight. March 31, 2016 Getting started March 31, 2016 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com Getting started

More information

ICM-Chemist-Pro How-To Guide. Version 3.6-1h Last Updated 12/29/2009

ICM-Chemist-Pro How-To Guide. Version 3.6-1h Last Updated 12/29/2009 ICM-Chemist-Pro How-To Guide Version 3.6-1h Last Updated 12/29/2009 ICM-Chemist-Pro ICM 3D LIGAND EDITOR: SETUP 1. Read in a ligand molecule or PDB file. How to setup the ligand in the ICM 3D Ligand Editor.

More information

Dock Ligands from a 2D Molecule Sketch

Dock Ligands from a 2D Molecule Sketch Dock Ligands from a 2D Molecule Sketch March 31, 2016 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com

More information

ICM-Chemist How-To Guide. Version 3.6-1g Last Updated 12/01/2009

ICM-Chemist How-To Guide. Version 3.6-1g Last Updated 12/01/2009 ICM-Chemist How-To Guide Version 3.6-1g Last Updated 12/01/2009 ICM-Chemist HOW TO IMPORT, SKETCH AND EDIT CHEMICALS How to access the ICM Molecular Editor. 1. Click here 2. Start sketching How to sketch

More information

You w i ll f ol l ow these st eps : Before opening files, the S c e n e panel is active.

You w i ll f ol l ow these st eps : Before opening files, the S c e n e panel is active. You w i ll f ol l ow these st eps : A. O pen a n i m a g e s t a c k. B. Tr a c e t h e d e n d r i t e w i t h t h e user-guided m ode. C. D e t e c t t h e s p i n e s a u t o m a t i c a l l y. D. C

More information

Tutorial: Structural Analysis of a Protein-Protein Complex

Tutorial: Structural Analysis of a Protein-Protein Complex Molecular Modeling Section (MMS) Department of Pharmaceutical and Pharmacological Sciences University of Padova Via Marzolo 5-35131 Padova (IT) @contact: stefano.moro@unipd.it Tutorial: Structural Analysis

More information

NMR Predictor. Introduction

NMR Predictor. Introduction NMR Predictor This manual gives a walk-through on how to use the NMR Predictor: Introduction NMR Predictor QuickHelp NMR Predictor Overview Chemical features GUI features Usage Menu system File menu Edit

More information

Preparing a PDB File

Preparing a PDB File Figure 1: Schematic view of the ligand-binding domain from the vitamin D receptor (PDB file 1IE9). The crystallographic waters are shown as small spheres and the bound ligand is shown as a CPK model. HO

More information

Version 1.2 October 2017 CSD v5.39

Version 1.2 October 2017 CSD v5.39 Mogul Geometry Check Table of Contents Introduction... 2 Example 1. Using Mogul to assess intramolecular geometry... 3 Example 2. Using Mogul to explain activity data... 5 Conclusions... 8 Further Exercises...

More information

Introduction to Structure Preparation and Visualization

Introduction to Structure Preparation and Visualization Introduction to Structure Preparation and Visualization Created with: Release 2018-4 Prerequisites: Release 2018-2 or higher Access to the internet Categories: Molecular Visualization, Structure-Based

More information

Application Note. U. Heat of Formation of Ethyl Alcohol and Dimethyl Ether. Introduction

Application Note. U. Heat of Formation of Ethyl Alcohol and Dimethyl Ether. Introduction Application Note U. Introduction The molecular builder (Molecular Builder) is part of the MEDEA standard suite of building tools. This tutorial provides an overview of the Molecular Builder s basic functionality.

More information

Molecular Modeling and Conformational Analysis with PC Spartan

Molecular Modeling and Conformational Analysis with PC Spartan Molecular Modeling and Conformational Analysis with PC Spartan Introduction Molecular modeling can be done in a variety of ways, from using simple hand-held models to doing sophisticated calculations on

More information

How to create a new geodatabase using the extract data wizard. 1. How to Extract the Schema to create a Geodatabase using an existing design.

How to create a new geodatabase using the extract data wizard. 1. How to Extract the Schema to create a Geodatabase using an existing design. How to create a new geodatabase using the extract data wizard The Extract Data Wizard can be used to create a new database based on an existing geodatabase. This tool may be used in the following cases:

More information

Building small molecules

Building small molecules Building small molecules Use the Builder (right panel) to build up molecules. Start building clicking a fragment/atom in the builder and it will appear to the workspace. Continue modifying the molecule

More information

Docking with Water in the Binding Site using GOLD

Docking with Water in the Binding Site using GOLD Docking with Water in the Binding Site using GOLD Version 2.0 November 2017 GOLD v5.6 Table of Contents Docking with Water in the Binding Site... 2 Case Study... 3 Introduction... 3 Provided Input Files...

More information

Exercises for Windows

Exercises for Windows Exercises for Windows CAChe User Interface for Windows Select tool Application window Document window (workspace) Style bar Tool palette Select entire molecule Select Similar Group Select Atom tool Rotate

More information

ISIS/Draw "Quick Start"

ISIS/Draw Quick Start ISIS/Draw "Quick Start" Click to print, or click Drawing Molecules * Basic Strategy 5.1 * Drawing Structures with Template tools and template pages 5.2 * Drawing bonds and chains 5.3 * Drawing atoms 5.4

More information

3D Molecule Viewer of MOGADOC (JavaScript)

3D Molecule Viewer of MOGADOC (JavaScript) 3D Molecule Viewer of MOGADOC (JavaScript) Movement of the Molecule Rotation of the molecule: Use left mouse button to drag. Translation of the molecule: Use right mouse button to drag. Resize the molecule:

More information

How to Make or Plot a Graph or Chart in Excel

How to Make or Plot a Graph or Chart in Excel This is a complete video tutorial on How to Make or Plot a Graph or Chart in Excel. To make complex chart like Gantt Chart, you have know the basic principles of making a chart. Though I have used Excel

More information

v Prerequisite Tutorials GSSHA WMS Basics Watershed Delineation using DEMs and 2D Grid Generation Time minutes

v Prerequisite Tutorials GSSHA WMS Basics Watershed Delineation using DEMs and 2D Grid Generation Time minutes v. 10.1 WMS 10.1 Tutorial GSSHA WMS Basics Creating Feature Objects and Mapping Attributes to the 2D Grid Populate hydrologic parameters in a GSSHA model using land use and soil data Objectives This tutorial

More information

Introduction to Spark

Introduction to Spark 1 As you become familiar or continue to explore the Cresset technology and software applications, we encourage you to look through the user manual. This is accessible from the Help menu. However, don t

More information

Pymol Practial Guide

Pymol Practial Guide Pymol Practial Guide Pymol is a powerful visualizor very convenient to work with protein molecules. Its interface may seem complex at first, but you will see that with a little practice is simple and powerful

More information

Performing a Pharmacophore Search using CSD-CrossMiner

Performing a Pharmacophore Search using CSD-CrossMiner Table of Contents Introduction... 2 CSD-CrossMiner Terminology... 2 Overview of CSD-CrossMiner... 3 Searching with a Pharmacophore... 4 Performing a Pharmacophore Search using CSD-CrossMiner Version 2.0

More information

Space Objects. Section. When you finish this section, you should understand the following:

Space Objects. Section. When you finish this section, you should understand the following: GOLDMC02_132283433X 8/24/06 2:21 PM Page 97 Section 2 Space Objects When you finish this section, you should understand the following: How to create a 2D Space Object and label it with a Space Tag. How

More information

(THIS IS AN OPTIONAL BUT WORTHWHILE EXERCISE)

(THIS IS AN OPTIONAL BUT WORTHWHILE EXERCISE) PART 2: Analysis in ArcGIS (THIS IS AN OPTIONAL BUT WORTHWHILE EXERCISE) Step 1: Start ArcCatalog and open a geodatabase If you have a shortcut icon for ArcCatalog on your desktop, double-click it to start

More information

Creating a Pharmacophore Query from a Reference Molecule & Scaffold Hopping in CSD-CrossMiner

Creating a Pharmacophore Query from a Reference Molecule & Scaffold Hopping in CSD-CrossMiner Table of Contents Creating a Pharmacophore Query from a Reference Molecule & Scaffold Hopping in CSD-CrossMiner Introduction... 2 CSD-CrossMiner Terminology... 2 Overview of CSD-CrossMiner... 3 Features

More information

The Quantizing functions

The Quantizing functions The Quantizing functions What is quantizing? Quantizing in its fundamental form is a function that automatically moves recorded notes, positioning them on exact note values: For example, if you record

More information

Comparing whole genomes

Comparing whole genomes BioNumerics Tutorial: Comparing whole genomes 1 Aim The Chromosome Comparison window in BioNumerics has been designed for large-scale comparison of sequences of unlimited length. In this tutorial you will

More information

User Guide (Windows and Macintosh)

User Guide (Windows and Macintosh) User Guide (Windows and Macintosh) WAVEFUNCTION Wavefunction, Inc. 18401 Von Karman Avenue, Suite 370 Irvine, CA 92612 U.S.A. www.wavefun.com Wavefunction, Inc., Japan Branch Office 3-5-2, Kouji-machi,

More information

Let s continue our discussion on the interaction between Fe(III) and 6,7-dihydroxynaphthalene-2- sulfonate.

Let s continue our discussion on the interaction between Fe(III) and 6,7-dihydroxynaphthalene-2- sulfonate. Chemistry 5995(133)-8990(013) Bioinorganic Chemistry: The Good, the Bad, and the Potential of Metals Assignment 2- Aqueous Speciation, Magnetism, Redox, UV-Vis Spectroscopy, and Pymol Let s continue our

More information

Watershed Modeling Orange County Hydrology Using GIS Data

Watershed Modeling Orange County Hydrology Using GIS Data v. 10.0 WMS 10.0 Tutorial Watershed Modeling Orange County Hydrology Using GIS Data Learn how to delineate sub-basins and compute soil losses for Orange County (California) hydrologic modeling Objectives

More information

Online Protein Structure Analysis with the Bio3D WebApp

Online Protein Structure Analysis with the Bio3D WebApp Online Protein Structure Analysis with the Bio3D WebApp Lars Skjærven, Shashank Jariwala & Barry J. Grant August 13, 2015 (updated November 17, 2016) Bio3D1 is an established R package for structural bioinformatics

More information

PQSMol. User s Manual

PQSMol. User s Manual PQSMol User s Manual c Parallel Quantum Solutions, 2006 www.pqs-chem.com Conventions used in this manual Filenames, commands typed in at the command prompt are written in typewriter font: pqsview aspirin.out

More information

41. Sim Reactions Example

41. Sim Reactions Example HSC Chemistry 7.0 41-1(6) 41. Sim Reactions Example Figure 1: Sim Reactions Example, Run mode view after calculations. General This example contains instruction how to create a simple model. The example

More information

Part 7 Bonds and Structural Supports

Part 7 Bonds and Structural Supports Part 7 Bonds and Structural Supports http://cbm.msoe.edu/newwebsite/learntomodel Introduction In addition to covalent bonds between atoms in a molecule, Jmol has the ability to render Hydrogen Bonds and

More information

Cres s et Bi omol ecul a r Di s covery Ltd, a l l ri ghts res erved.

Cres s et Bi omol ecul a r Di s covery Ltd, a l l ri ghts res erved. 10.5 2017 Cres s et Bi omol ecul a r Di s covery Ltd, a l l ri ghts res erved. Table of contents Introduction... 8 What are field points?... 8 Interpretation of field point patterns... 9 About this document...

More information

McIDAS-V Tutorial Displaying Point Observations from ADDE Datasets updated July 2016 (software version 1.6)

McIDAS-V Tutorial Displaying Point Observations from ADDE Datasets updated July 2016 (software version 1.6) McIDAS-V Tutorial Displaying Point Observations from ADDE Datasets updated July 2016 (software version 1.6) McIDAS-V is a free, open source, visualization and data analysis software package that is the

More information

VCell Tutorial. Building a Rule-Based Model

VCell Tutorial. Building a Rule-Based Model VCell Tutorial Building a Rule-Based Model We will demonstrate how to create a rule-based model of EGFR receptor interaction with two adapter proteins Grb2 and Shc. A Receptor-monomer reversibly binds

More information

Introduction to ArcMap

Introduction to ArcMap Introduction to ArcMap ArcMap ArcMap is a Map-centric GUI tool used to perform map-based tasks Mapping Create maps by working geographically and interactively Display and present Export or print Publish

More information

Molecular Visualization. Introduction

Molecular Visualization. Introduction Molecular Visualization Jeffry D. Madura Department of Chemistry & Biochemistry Center for Computational Sciences Duquesne University Introduction Assessments of change, dynamics, and cause and effect

More information

Introduction to Hartree-Fock calculations in Spartan

Introduction to Hartree-Fock calculations in Spartan EE5 in 2008 Hannes Jónsson Introduction to Hartree-Fock calculations in Spartan In this exercise, you will get to use state of the art software for carrying out calculations of wavefunctions for molecues,

More information

Tutorial 12 Excess Pore Pressure (B-bar method) Undrained loading (B-bar method) Initial pore pressure Excess pore pressure

Tutorial 12 Excess Pore Pressure (B-bar method) Undrained loading (B-bar method) Initial pore pressure Excess pore pressure Tutorial 12 Excess Pore Pressure (B-bar method) Undrained loading (B-bar method) Initial pore pressure Excess pore pressure Introduction This tutorial will demonstrate the Excess Pore Pressure (Undrained

More information

ESCI 121 Physical Geology

ESCI 121 Physical Geology Observing Streams & Rivers in Google Earth Dr. Jennifer L. Piatek Dept. of Physics and Earth Sciences Central Connecticut State University 506 Copernicus Hall 1615 Stanley Street New Britain, CT 06050

More information

Flexibility and Constraints in GOLD

Flexibility and Constraints in GOLD Flexibility and Constraints in GOLD Version 2.1 August 2018 GOLD v5.6.3 Table of Contents Purpose of Docking... 3 GOLD s Evolutionary Algorithm... 4 GOLD and Hermes... 4 Handling Flexibility and Constraints

More information

10. Facies Modeling Sequential Indicator Simulation (SIS)

10. Facies Modeling Sequential Indicator Simulation (SIS) 10. Facies Modeling 10.1 Sequential Indicator Simulation (SIS) In this section the process of building a basic facies model conditioned to well observations using SIS. The variogram type, ranges, and azimuth

More information

Pose Prediction with GOLD

Pose Prediction with GOLD Pose Prediction with GOLD Version 3.0 November 2018 GOLD v5.7.0 Table of Contents The Purpose of Docking... 2 GOLD s Evolutionary Algorithm... 3 A Checklist for Docking... 3 GOLD and Hermes... 3 Redocking

More information

1 Introduction to Computational Chemistry (Spartan)

1 Introduction to Computational Chemistry (Spartan) 1 Introduction to Computational Chemistry (Spartan) Start Spartan by clicking Start / Programs / Spartan Then click File / New Exercise 1 Study of H-X-H Bond Angles (Suitable for general chemistry) Structure

More information

The Rain in Spain - Tableau Public Workbook

The Rain in Spain - Tableau Public Workbook The Rain in Spain - Tableau Public Workbook This guide will take you through the steps required to visualize how the rain falls in Spain with Tableau public. (All pics from Mac version of Tableau) Workbook

More information

APBS electrostatics in VMD - Software. APBS! >!Examples! >!Visualization! >! Contents

APBS electrostatics in VMD - Software. APBS! >!Examples! >!Visualization! >! Contents Software Search this site Home Announcements An update on mailing lists APBS 1.2.0 released APBS 1.2.1 released APBS 1.3 released New APBS 1.3 Windows Installer PDB2PQR 1.7.1 released PDB2PQR 1.8 released

More information

Molecular modeling with InsightII

Molecular modeling with InsightII Molecular modeling with InsightII Yuk Sham Computational Biology/Biochemistry Consultant Phone: (612) 624 7427 (Walter Library) Phone: (612) 624 0783 (VWL) Email: shamy@msi.umn.edu How to run InsightII

More information

Bonds and Structural Supports

Bonds and Structural Supports Bonds and Structural Supports Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingresources/jmol/jmoltraining/struts.html

More information

The Hückel Approximation Consider a conjugated molecule i.e. a molecule with alternating double and single bonds, as shown in Figure 1.

The Hückel Approximation Consider a conjugated molecule i.e. a molecule with alternating double and single bonds, as shown in Figure 1. The Hückel Approximation In this exercise you will use a program called Hückel to look at the p molecular orbitals in conjugated molecules. The program calculates the energies and shapes of p (pi) molecular

More information

Assignment 1: Molecular Mechanics (PART 1 25 points)

Assignment 1: Molecular Mechanics (PART 1 25 points) Chemistry 380.37 Fall 2015 Dr. Jean M. Standard August 19, 2015 Assignment 1: Molecular Mechanics (PART 1 25 points) In this assignment, you will perform some molecular mechanics calculations using the

More information

OneStop Map Viewer Navigation

OneStop Map Viewer Navigation OneStop Map Viewer Navigation» Intended User: Industry Map Viewer users Overview The OneStop Map Viewer is an interactive map tool that helps you find and view information associated with energy development,

More information

Introduction to Astronomy Laboratory Exercise #1. Intro to the Sky

Introduction to Astronomy Laboratory Exercise #1. Intro to the Sky Introduction to Astronomy Laboratory Exercise #1 Partners Intro to the Sky Date Section Purpose: To develop familiarity with the daytime and nighttime sky through the use of Stellarium. Equipment: Computer

More information

Section III - Designing Models for 3D Printing

Section III - Designing Models for 3D Printing Section III - Designing Models for 3D Printing In this section of the Jmol Training Guide, you will become familiar with the commands needed to design a model that will be built on a 3D Printer. As you

More information

Chem 253. Tutorial for Materials Studio

Chem 253. Tutorial for Materials Studio Chem 253 Tutorial for Materials Studio This tutorial is designed to introduce Materials Studio 7.0, which is a program used for modeling and simulating materials for predicting and rationalizing structure

More information

MassHunter Software Overview

MassHunter Software Overview MassHunter Software Overview 1 Qualitative Analysis Workflows Workflows in Qualitative Analysis allow the user to only see and work with the areas and dialog boxes they need for their specific tasks A

More information

Calculating Bond Enthalpies of the Hydrides

Calculating Bond Enthalpies of the Hydrides Proposed Exercise for the General Chemistry Section of the Teaching with Cache Workbook: Calculating Bond Enthalpies of the Hydrides Contributed by James Foresman, Rachel Fogle, and Jeremy Beck, York College

More information

Automatic Watershed Delineation using ArcSWAT/Arc GIS

Automatic Watershed Delineation using ArcSWAT/Arc GIS Automatic Watershed Delineation using ArcSWAT/Arc GIS By: - Endager G. and Yalelet.F 1. Watershed Delineation This tool allows the user to delineate sub watersheds based on an automatic procedure using

More information

Viewing and Analyzing Proteins, Ligands and their Complexes 2

Viewing and Analyzing Proteins, Ligands and their Complexes 2 2 Viewing and Analyzing Proteins, Ligands and their Complexes 2 Overview Viewing the accessible surface Analyzing the properties of proteins containing thousands of atoms is best accomplished by representing

More information

HSC Chemistry 7.0 User's Guide

HSC Chemistry 7.0 User's Guide HSC Chemistry 7.0 47-1 HSC Chemistry 7.0 User's Guide Sim Flowsheet Module Experimental Mode Pertti Lamberg Outotec Research Oy Information Service P.O. Box 69 FIN - 28101 PORI, FINLAND Fax: +358-20 -

More information

TECDIS and TELchart ECS Weather Overlay Guide

TECDIS and TELchart ECS Weather Overlay Guide 1 of 24 TECDIS and TELchart ECS provides a very advanced weather overlay feature, using top quality commercial maritime weather forecast data available as a subscription service from Jeppesen Marine. The

More information

WMS 9.0 Tutorial GSSHA Modeling Basics Infiltration Learn how to add infiltration to your GSSHA model

WMS 9.0 Tutorial GSSHA Modeling Basics Infiltration Learn how to add infiltration to your GSSHA model v. 9.0 WMS 9.0 Tutorial GSSHA Modeling Basics Infiltration Learn how to add infiltration to your GSSHA model Objectives This workshop builds on the model developed in the previous workshop and shows you

More information

This tutorial is intended to familiarize you with the Geomatica Toolbar and describe the basics of viewing data using Geomatica Focus.

This tutorial is intended to familiarize you with the Geomatica Toolbar and describe the basics of viewing data using Geomatica Focus. PCI GEOMATICS GEOMATICA QUICKSTART 1. Introduction This tutorial is intended to familiarize you with the Geomatica Toolbar and describe the basics of viewing data using Geomatica Focus. All data used in

More information

Protein Bioinformatics Computer lab #1 Friday, April 11, 2008 Sean Prigge and Ingo Ruczinski

Protein Bioinformatics Computer lab #1 Friday, April 11, 2008 Sean Prigge and Ingo Ruczinski Protein Bioinformatics 260.655 Computer lab #1 Friday, April 11, 2008 Sean Prigge and Ingo Ruczinski Goals: Approx. Time [1] Use the Protein Data Bank PDB website. 10 minutes [2] Use the WebMol Viewer.

More information

Computer simulation of radioactive decay

Computer simulation of radioactive decay Computer simulation of radioactive decay y now you should have worked your way through the introduction to Maple, as well as the introduction to data analysis using Excel Now we will explore radioactive

More information

MAGNETITE OXIDATION EXAMPLE

MAGNETITE OXIDATION EXAMPLE HSC Chemistry 7.0 1 MAGNETITE OXIDATION EXAMPLE Pelletized magnetite (Fe 3 O 4 ) ore may be oxidized to hematite (Fe 2 O 3 ) in shaft furnace. Typical magnetite content in ore is some 95%. Oxidation is

More information

Assignment #0 Using Stellarium

Assignment #0 Using Stellarium Name: Class: Date: Assignment #0 Using Stellarium The purpose of this exercise is to familiarize yourself with the Stellarium program and its many capabilities and features. Stellarium is a visually beautiful

More information

ncounter PlexSet Data Analysis Guidelines

ncounter PlexSet Data Analysis Guidelines ncounter PlexSet Data Analysis Guidelines NanoString Technologies, Inc. 530 airview Ave North Seattle, Washington 98109 USA Telephone: 206.378.6266 888.358.6266 E-mail: info@nanostring.com Molecules That

More information

Example: Identification

Example: Identification Example: Identification In this structure we will explore Atom identification Working with maps Working with projections Eliminating diffusely diffracting solvent Disorder modeling Restrain application

More information

An Instructional Module. FieldScope Unit 1. Introduction to National Geographic Society s FieldScope Program.

An Instructional Module. FieldScope Unit 1. Introduction to National Geographic Society s FieldScope Program. An Instructional Module FieldScope Unit 1 www.budburst.org/fieldscope Introduction to National Geographic Society s FieldScope Program Unit Contents Overview 3 Learning Objectives Time Commitment Technical

More information

M E R C E R W I N WA L K T H R O U G H

M E R C E R W I N WA L K T H R O U G H H E A L T H W E A L T H C A R E E R WA L K T H R O U G H C L I E N T S O L U T I O N S T E A M T A B L E O F C O N T E N T 1. Login to the Tool 2 2. Published reports... 7 3. Select Results Criteria...

More information

Ensemble Docking with GOLD

Ensemble Docking with GOLD Ensemble Docking with GOLD Version 2.0 November 2017 GOLD v5.6 Table of Contents Ensemble Docking... 2 Case Study... 3 Introduction... 3 Provided Input Files... 5 Superimposing Protein Structures... 6

More information

Jasco V-670 absorption spectrometer

Jasco V-670 absorption spectrometer Laser Spectroscopy Labs Jasco V-670 absorption spectrometer Operation instructions 1. Turn ON the power switch on the right side of the spectrophotometer. It takes about 5 minutes for the light source

More information

How to Create a Substance Answer Set

How to Create a Substance Answer Set How to Create a Substance Answer Set Select among five search techniques to find substances Since substances can be described by multiple names or other characteristics, SciFinder gives you the flexibility

More information

1. Open IDV. There is a desktop link, choose version 3.0u1 or 3.0u2. It can take a few minutes to open.

1. Open IDV. There is a desktop link, choose version 3.0u1 or 3.0u2. It can take a few minutes to open. Page 1 Objectives: Become familiar with using a software package (IDV) to view satellite images Understand the differences between Visible, IR, and Microwave Imagery Observe the influence of dry air and

More information

OECD QSAR Toolbox v.4.1. Tutorial illustrating new options for grouping with metabolism

OECD QSAR Toolbox v.4.1. Tutorial illustrating new options for grouping with metabolism OECD QSAR Toolbox v.4.1 Tutorial illustrating new options for grouping with metabolism Outlook Background Objectives Specific Aims The exercise Workflow 2 Background Grouping with metabolism is a procedure

More information

Enhanced Mapping. RP Data Professional. What you will learn in this guide. CoreLogic RP Data Professional Getting Started Guide Series

Enhanced Mapping. RP Data Professional. What you will learn in this guide. CoreLogic RP Data Professional Getting Started Guide Series RP Data Professional Enhanced Mapping What you will learn in this guide This guide will show you how to use RP Data Professional enhanced mapping capabilities to research and present details about a target

More information

Using Feature Templates for Complex Editing

Using Feature Templates for Complex Editing Using Feature Templates for Complex Editing By Mike Price, Entrada/San Juan, Inc. What You Will Need ArcGIS 10.3 for Desktop (Basic, Standard, or Advanced license) Sample dataset downloaded from esri.com/arcuser

More information

Chemistry 14CL. Worksheet for the Molecular Modeling Workshop. (Revised FULL Version 2012 J.W. Pang) (Modified A. A. Russell)

Chemistry 14CL. Worksheet for the Molecular Modeling Workshop. (Revised FULL Version 2012 J.W. Pang) (Modified A. A. Russell) Chemistry 14CL Worksheet for the Molecular Modeling Workshop (Revised FULL Version 2012 J.W. Pang) (Modified A. A. Russell) Structure of the Molecular Modeling Assignment The molecular modeling assignment

More information

The Kalzium Handbook. Carsten Niehaus

The Kalzium Handbook. Carsten Niehaus Carsten Niehaus 2 Contents 1 Introduction 1 2 Kalzium quick start guide 2 3 Using Kalzium 6 3.1 Overview of Kalziums usage.................... 6 3.2 The information dialog........................ 6 3.2.1

More information

The Geodatabase Working with Spatial Analyst. Calculating Elevation and Slope Values for Forested Roads, Streams, and Stands.

The Geodatabase Working with Spatial Analyst. Calculating Elevation and Slope Values for Forested Roads, Streams, and Stands. GIS LAB 7 The Geodatabase Working with Spatial Analyst. Calculating Elevation and Slope Values for Forested Roads, Streams, and Stands. This lab will ask you to work with the Spatial Analyst extension.

More information

Patrick: An Introduction to Medicinal Chemistry 5e MOLECULAR MODELLING EXERCISES CHAPTER 17

Patrick: An Introduction to Medicinal Chemistry 5e MOLECULAR MODELLING EXERCISES CHAPTER 17 MOLECULAR MODELLING EXERCISES CHAPTER 17 Exercise 17.6 Conformational analysis of n-butane Introduction Figure 1 Butane Me Me In this exercise, we will consider the possible stable conformations of butane

More information

Computational Chemistry Lab Module: Conformational Analysis of Alkanes

Computational Chemistry Lab Module: Conformational Analysis of Alkanes Introduction Computational Chemistry Lab Module: Conformational Analysis of Alkanes In this experiment, we will use CAChe software package to model the conformations of butane, 2-methylbutane, and substituted

More information

Refine & Validate. In the *.res file, be sure to add the following four commands after the UNIT instruction and before any atoms: ACTA CONF WPDB -2

Refine & Validate. In the *.res file, be sure to add the following four commands after the UNIT instruction and before any atoms: ACTA CONF WPDB -2 Refine & Validate Refinement is simply a way to improve the fit between the measured intensities and the intensities calculated from the model. The peaks in the difference map and the list of worst fitting

More information

Autodock tutorial VINA with UCSF Chimera

Autodock tutorial VINA with UCSF Chimera Autodock tutorial VINA with UCSF Chimera José R. Valverde CNB/CSIC jrvalverde@cnb.csic.es José R. Valverde, 2014 CC-BY-NC-SA Loading the receptor Open UCSF Chimera and then load the protein: File Open

More information

User Guide. Affirmatively Furthering Fair Housing Data and Mapping Tool. U.S. Department of Housing and Urban Development

User Guide. Affirmatively Furthering Fair Housing Data and Mapping Tool. U.S. Department of Housing and Urban Development User Guide Affirmatively Furthering Fair Housing Data and Mapping Tool U.S. Department of Housing and Urban Development December, 2015 1 Table of Contents 1. Getting Started... 5 1.1 Software Version...

More information

Eurostat Business Cycle Clock (BCC): A user's guide

Eurostat Business Cycle Clock (BCC): A user's guide EUROPEAN COMMISSION EUROSTAT Directorate C: National Accounts, Prices and Key Indicators Unit C-1: National accounts methodology. Indicators ESTAT.C.1 - National accounts methodology/indicators Eurostat

More information

Chem 1 Kinetics. Objectives. Concepts

Chem 1 Kinetics. Objectives. Concepts Chem 1 Kinetics Objectives 1. Learn some basic ideas in chemical kinetics. 2. Understand how the computer visualizations can be used to benefit the learning process. 3. Understand how the computer models

More information

Endothermic and Exothermic Reactions

Endothermic and Exothermic Reactions Endothermic and Exothermic Reactions Experiment 1 Many chemical reactions give off energy. Chemical reactions that release energy are called exothermic reactions. Some chemical reactions absorb energy

More information

In this exercise we will learn how to use the analysis tools in ArcGIS with vector and raster data to further examine potential building sites.

In this exercise we will learn how to use the analysis tools in ArcGIS with vector and raster data to further examine potential building sites. GIS Level 2 In the Introduction to GIS workshop we filtered data and visually examined it to determine where to potentially build a new mixed use facility. In order to get a low interest loan, the building

More information

23. Benson Module. HSC 8 Benson November 19, Research Center, Pori / Hannu Vuori, Lauri Mäenpää ORC-J 1 (12) 23.1.

23. Benson Module. HSC 8 Benson November 19, Research Center, Pori / Hannu Vuori, Lauri Mäenpää ORC-J 1 (12) 23.1. 23. Benson Module HSC 8 Benson 14016-ORC-J 1 (12) 23.1. Preface In spite of the vast extent of the comprehensive database included in HSC, which is the largest available in the commercial world, only a

More information

The Hückel Approximation

The Hückel Approximation The ückel Approximation 1 In this exercise you will use a program called ückel to look at the π molecular orbitals in conjugated molecules. The program calculates the energies and shapes of π (pi) molecular

More information

An area chart emphasizes the trend of each value over time. An area chart also shows the relationship of parts to a whole.

An area chart emphasizes the trend of each value over time. An area chart also shows the relationship of parts to a whole. Excel 2003 Creating a Chart Introduction Page 1 By the end of this lesson, learners should be able to: Identify the parts of a chart Identify different types of charts Create an Embedded Chart Create a

More information

IncuCyte ZOOM NeuroTrack Fluorescent Processing

IncuCyte ZOOM NeuroTrack Fluorescent Processing IncuCyte ZOOM NeuroTrack Fluorescent Processing The NeuroTrack TM Software Module (Cat No 9600-0011) is used to measure the processes of neurons in monoculture or with fluorescent labeling in co-culture.

More information

Starry Night Version 5.7 Features What s new and how to use them!

Starry Night Version 5.7 Features What s new and how to use them! Starry Night Version 5.7 Features What s new and how to use them! New Features Overview 1. Space Missions (Probe Paths) 2. 3-D Object Models 3. Advanced Telescope Control panel 4. Google Maps Integration

More information

Bloomsburg University Weather Viewer Quick Start Guide. Software Version 1.2 Date 4/7/2014

Bloomsburg University Weather Viewer Quick Start Guide. Software Version 1.2 Date 4/7/2014 Bloomsburg University Weather Viewer Quick Start Guide Software Version 1.2 Date 4/7/2014 Program Background / Objectives: The Bloomsburg Weather Viewer is a weather visualization program that is designed

More information

3D - Structure Graphics Capabilities with PDF-4 Database Products

3D - Structure Graphics Capabilities with PDF-4 Database Products 3D - Structure Graphics Capabilities with PDF-4 Database Products Atomic Structure Information in the PDF-4 Databases ICDD s PDF-4 databases contain atomic structure information for a significant number

More information