DOCSLIB.ORG

Open Babel Documentation Release 2.3.1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Open Babel Documentation Release 2.3.1 Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) February 28, 2012 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Generating conformers for structures .................................. 22 3.8 Filtering molecules from a multimolecule file .............................. 23 3.9 Substructure and similarity searching .................................. 25 3.10 Sorting molecules ............................................ 26 3.11 Remove duplicate molecules ....................................... 26 3.12 Aliases for chemical groups ....................................... 27 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options .................................................. 29 4.3 Multiple input files ............................................ 30 4.4 Wildcards in filenames .......................................... 30 4.5 Local input ................................................ 30 4.6 Output file ................................................ 30 4.7 Graphical display ............................................. 30 4.8 Using a restricted set of formats ..................................... 31 4.9 Other features .............................................. 31 4.10 Example files ............................................... 31 5 Molecular fingerprints and similarity searching 33 5.1 Fingerprint format ............................................ 33 5.2 Spectrophores™ ............................................. 37 6 obabel vs Chemistry Toolkit Rosetta 43 i 6.1 Heavy atom counts from an SD file ................................... 43 6.2 Convert a SMILES string to canonical SMILES ............................. 43 6.3 Report how many SD file records are within a certain molecular weight range ............. 44 6.4 Convert SMILES file to SD file ..................................... 44 6.5 Report the similarity between two structures .............................. 44 6.6 Find the 10 nearest neighbors in a data set ................................ 44 6.7 Depict a compound as an image ..................................... 45 6.8 Highlight a substructure in the depiction ................................. 45 6.9 Align the depiction using a fixed substructure .............................. 46 6.10 Perform a substructure search on an SDF file and report the number of false positives ......... 46 6.11 Calculate TPSA ............................................. 47 6.12 Working with SD tag data ........................................ 47 6.13 Unattempted tasks ............................................ 48 7 Write software using the Open Babel library 49 7.1 The Open Babel API ........................................... 49 7.2 C++ .................................................... 50 7.3 Python .................................................. 52 7.4 Java .................................................... 69 7.5 Perl .................................................... 72 7.6 CSharp and OBDotNet .......................................... 75 7.7 Ruby ................................................... 77 8 Cheminformatics 101 79 8.1 Cheminformatics Basics ......................................... 79 8.2 Representing Molecules ......................................... 81 8.3 Substructure Searching with Indexes .................................. 85 8.4 Molecular Similarity ........................................... 86 8.5 Chemical Registration Systems ..................................... 87 9 Radicals and SMILES extensions 89 9.1 The need for radicals and implicit hydrogen to coexist ......................... 89 9.2 How Open Babel does it ......................................... 89 9.3 In radicals either the hydrogen or the spin multiplicity can be implicit ................. 90 9.4 SMILES extensions for radicals ..................................... 90 10 Contributing to Open Babel 93 10.1 Overview ................................................. 93 10.2 Developing Open Babel ......................................... 94 10.3 Documentation .............................................. 99 10.4 Testing the Code ............................................. 100 10.5 Software Archaeology .......................................... 101 11 Adding plugins 103 11.1 How to add a new file format ...................................... 103 11.2 Adding new operations and options ................................... 104 12 Supported File Formats and Options 107 12.1 Common cheminformatics formats ................................... 107 12.2 Utility formats .............................................. 113 12.3 Other cheminformatics formats ..................................... 122 12.4 Computational chemistry formats .................................... 123 12.5 Crystallography formats ......................................... 130 12.6 Reaction formats ............................................. 132 12.7 Image formats .............................................. 133 ii 12.8 2D drawing formats ........................................... 138 12.9 3D viewer formats ............................................ 138 12.10 Kinetics and Thermodynamics formats ................................. 139 12.11 Molecular dynamics and docking formats ................................ 140 12.12 Volume data formats ........................................... 142 12.13 Miscellaneous formats .......................................... 143 12.14 Biological data formats .......................................... 143 12.15 Obscure formats ............................................. 143 Bibliography 145 iii iv Open Babel Documentation, Release 2.3.1 The latest version of this documentation is available in several formats from http://openbabel.org/docs/dev/. Contents 1 Open Babel Documentation, Release 2.3.1 2 Contents Chapter 1 Introduction Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. 1.1 Goals of the Open Babel project Open Babel is a project to facilitate the interconversion of chemical data from one format to another – including file formats of various types. This is important for the following reasons: • Multiple programs are often required in realistic workflows. These may include databases, modeling or compu- tational programs, visualization programs, etc. • Many programs have individual data formats, and/or support only a small subset of other file types. • Chemical representations often vary considerably: – Some programs are 2D. Some are 3D. Some use fractional k-space coordinates. – Some programs use bonds and atoms of discrete types. Others use only atoms and electrons. – Some programs use symmetric representations. Others do not. – Some programs specify all atoms. Others use “residues” or omit hydrogen atoms. • Individual implementations of even standardized file formats are often buggy, incomplete or do not completely match published standards. As a free, and open source project, Open Babel improves by way of helping others. It gains by way of its users, contributors, developers, related projects, and the general chemical community. We must continually strive to support these constituencies. We gratefully accept contributions in many forms – from bug reports, complaints, and critiques, which help us improve what we do poorly, to feature suggestions, code contributions, and other efforts, which direct our future development. • For end users, we seek to provide a range of utility, from simple (or complex) file interconversion, to indexing, databasing, and transforming chemical and molecular data. • For developers, we seek to provide an easy-to-use free and open source chemical library. This assists a variety of chemical software, from molecular viewers and visualization tools and editors to databases, property prediction tools, and in-house development. To this end, we hope that our tools reflect several key points: • As much chemical information and files should be read and understood by Open Babel. This means that we should always strive to support as many concepts as possible in a given file format, and support for additional file formats is beneficial to the community as a whole. • Releases should be made to be “as good as we can make it” each and every time. 3 Open Babel Documentation, Release 2.3.1 • Improving our code and our community to bring in additional contributions in many forms helps both developers and end-users alike. Making development
Load more

Recommended publications
  • Open Babel Documentation Release 2.3.1
    Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options .................................................
    [Show full text]
  • Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
    Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al.
    [Show full text]
  • The Alexandria Library, a Quantum-Chemical Database of Molecular Properties for Force field Development 9 2017 Received: October 1 1 1 Mohammad M
    www.nature.com/scientificdata OPEN Data Descriptor: The Alexandria library, a quantum-chemical database of molecular properties for force field development 9 2017 Received: October 1 1 1 Mohammad M. Ghahremanpour , Paul J. van Maaren & David van der Spoel Accepted: 19 February 2018 Published: 10 April 2018 Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules. Design Type(s) data integration objective • molecular physical property analysis objective Measurement Type(s) physicochemical characterization Technology Type(s) Computational Chemistry Factor Type(s) Sample Characteristic(s) 1 Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden. Correspondence and requests for materials should be addressed to D.v.d.S. (email: [email protected]).
    [Show full text]
  • Structural Insight Into Pichia Pastoris Fatty Acid Synthase Joseph S
    www.nature.com/scientificreports OPEN Structural insight into Pichia pastoris fatty acid synthase Joseph S. Snowden, Jehad Alzahrani, Lee Sherry, Martin Stacey, David J. Rowlands, Neil A. Ranson* & Nicola J. Stonehouse* Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identifed FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purifed from P. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure of P. pastoris FAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identifed several diferences in both structural and enzymatic domains through comparison with the prototypical yeast FAS from S. cerevisiae. Using focussed classifcation, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further eforts to engineer yeast FAS for synthesis of alternate products. Fatty acid synthases (FASs) are critical metabolic enzymes for the endogenous biosynthesis of fatty acids in a diverse range of organisms. Trough iterative cycles of chain elongation, FASs catalyse the synthesis of long-chain fatty acids that can produce raw materials for membrane bilayer synthesis, lipid anchors of peripheral membrane proteins, metabolic energy stores, or precursors for various fatty acid-derived signalling compounds1. In addition to their key physiological importance, microbial FAS systems are also a common target of metabolic engineering approaches, usually with the aim of generating short chain fatty acids for an expanded repertoire of fatty acid- derived chemicals, including chemicals with key industrial signifcance such as α-olefns2–6.
    [Show full text]
  • JRC QSAR Model Database
    JRC QSAR Model Database EURL ECVAM DataBase service on ALternative Methods to animal experimentation To promote the development and uptake of alternative and advanced methods in toxicology and biomedical sciences SDF - STRUCTURE DATA FORMAT: How to create from SMILES The European Commission’s science and knowledge service Joint Research Centre Directorate F Health, Consumers & Reference Materials Chemicals Safety & Alternative Methods Unit The European Commission’s science and knowledge service Joint Research Centre EUR 28708 EN This publication is a Tutorial by the Joint Research Centre (JRC), the European Commission’s science and knowledge service. It aims to provide user support. The scientific output expressed does not imply a policy position of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of this publication. Contact information Email: [email protected] JRC Science Hub https://ec.europa.eu/jrc JRC107492 EUR 28708 EN PDF ISBN 978-92-79-71294-4 ISSN 1831-9424 doi:10.2760/952280 Print ISBN 978-92-79-71295-1 ISSN 1018-5593 doi:10.2760/668595 Luxembourg: Publications Office of the European Union, 2017 Ispra: European Commission, 2017 © European Union, 2017 The reuse of the document is authorised, provided the source is acknowledged and the original meaning or message of the texts are not distorted. The European Commission shall not be held liable for any consequences stemming from the reuse. How to cite this document: Triebe
    [Show full text]
  • Computer-Assisted Catalyst Development Via Automated Modelling of Conformationally Complex Molecules
    www.nature.com/scientificreports OPEN Computer‑assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligands Sibo Lin1*, Jenna C. Fromer2, Yagnaseni Ghosh1, Brian Hanna1, Mohamed Elanany3 & Wei Xu4 Simulation of conformationally complicated molecules requires multiple levels of theory to obtain accurate thermodynamics, requiring signifcant researcher time to implement. We automate this workfow using all open‑source code (XTBDFT) and apply it toward a practical challenge: diphosphinoamine (PNP) ligands used for ethylene tetramerization catalysis may isomerize (with deleterious efects) to iminobisphosphines (PPNs), and a computational method to evaluate PNP ligand candidates would save signifcant experimental efort. We use XTBDFT to calculate the thermodynamic stability of a wide range of conformationally complex PNP ligands against isomeriation to PPN (ΔGPPN), and establish a strong correlation between ΔGPPN and catalyst performance. Finally, we apply our method to screen novel PNP candidates, saving signifcant time by ruling out candidates with non‑trivial synthetic routes and poor expected catalytic performance. Quantum mechanical methods with high energy accuracy, such as density functional theory (DFT), can opti- mize molecular input structures to a nearby local minimum, but calculating accurate reaction thermodynamics requires fnding global minimum energy structures1,2. For simple molecules, expert intuition can identify a few minima to focus study on, but an alternative approach must be considered for more complex molecules or to eventually fulfl the dream of autonomous catalyst design 3,4: the potential energy surface must be frst surveyed with a computationally efcient method; then minima from this survey must be refned using slower, more accurate methods; fnally, for molecules possessing low-frequency vibrational modes, those modes need to be treated appropriately to obtain accurate thermodynamic energies 5–7.
    [Show full text]
  • Quickly Documentation Release 0.1
    Quickly Documentation Release 0.1 Michael Spencer March 28, 2016 Contents 1 Offline Reading 3 1.1 Tutorial..................................................3 1.2 QMLify Transpiler............................................5 1.3 Core JS Modules.............................................5 1.4 Distributing your Module........................................8 2 Indices and tables 11 i ii Quickly Documentation, Release 0.1 Quickly is a build tool and QML module with provides an NodeJS-like ES6 environment for Javascript used in QML. The goal of the project is to allow you to write awesome modern ES6 Javascript taking advantage of classes, decorators, arrow functions, and best of all, many of the vast array of NPM packages available using the standard ES6 module imports. You can then take that code and use in directly from QML, just as you would with plain, old, QML-specific Javascript. You can even build a library using ES6 and NPM packages, and then distribute that as a standard QML module or QPM package for other developers to use in regular QML or QML-specific Javascript. For those who would prefer to stick with standard QML-specific Javascript, you can also do that and still use the Quickly library, which gives you promises, the fetch API, and many polyfills. This is great for longtime QML devel- opers or existing projects that just want to drop in some easy-to-use features from modern JS core libraries. Tutorial A quick guide to get you up and running with Quickly. QMLify Transpiler How to use qmlify, the Quickly transpiler. Core JS Modules How to use the core JS modules. Distributing your Module Distributing your awesome new module for other developers to use.
    [Show full text]
  • Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department
    Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department Name of FOSS Applications Employability GChemPaint GChemPaint is an editor for 2Dchem- GChemPaint is currently being developed ical structures with a multiple docu- as part of The Chemistry Development ment interface. Kit, and a Standard Widget Tool kit- based GChemPaint application is being developed, as part of Bioclipse. Jmol Jmol applet is used to explore the Jmol is a free, open source molecule viewer structure of molecules. Jmol applet is for students, educators, and researchers used to depict X-ray structures in chemistry and biochemistry. It is cross- platform, running on Windows, Mac OS X, and Linux/Unix systems. For PG Students LaTeX Document markup language and Value addition to academic Skills set. preparation system for Tex typesetting Essential for International paper presentation and scientific journals. For PG student for their project work Scilab Scientific Computation package for Value addition in technical problem numerical computations solving via use of computational methods for engineering problems, Applicable in Chemical, ECE, Electrical, Electronics, Civil, Mechanical, Mathematics etc. For PG student who are taking Physical Chemistry Avogadro Avogadro is a free and open source, Research and Development in Chemistry, advanced molecule editor and Pharmacist and University lecturers. visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc. Spoken Tutorial Project, IIT Bombay Brochure for Commerce and Commerce IT Name of FOSS Applications / Employability LibreOffice – Writer, Calc, Writing letters, documents, creating spreadsheets, tables, Impress making presentations, desktop publishing LibreOffice – Base, Draw, Managing databases, Drawing, doing simple Mathematical Math operations For Commerce IT Students Drupal Drupal is a free and open source content management system (CMS).
    [Show full text]
  • Copyrighted Material
    PART I METHODS COPYRIGHTED MATERIAL CHAPTER 1 Overview of Thermochemistry and Its Application to Reaction Kinetics ELKE GOOS Institute of Combustion Technology, German Aerospace Center (DLR), Stuttgart, Germany ALEXANDER BURCAT Faculty of Aerospace Engineering, Technion - Israel Institute of Technology, Haifa, Israel 1.1 HISTORY OF THERMOCHEMISTRY Thermochemistry deals with energy and enthalpy changes accompanying chemical reactions and phase transformations and gives a first estimate of whether a given reaction can occur. To our knowledge, the field of thermochemistry started with the experiments done by Malhard and Le Chatelier [1] with gunpowder and explosives. The first of their two papers of 1883 starts with the sentence: “All combustion is accompanied by the release of heat that increases the temperature of the burned bodies.” In 1897, Berthelot [2], who also experimented with explosives, published his two-volume monograph Thermochimie in which he summed up 40 years of calori- metric studies. The first textbook, to our knowledge, that clearly explained the principles of thermochemical properties was authored by Lewis and Randall [3] in 1923. Thermochemical data, actually heats of formation, were gathered, evaluated, and published for the first time in the seven-volume book International Critical Tables of Numerical Data, Physics, Chemistry and Technology [4] during 1926–1930 (and the additional index in 1933). In 1932, the American Chemical Society (ACS) monograph No. 60 The Free Energy of Some Organic Compounds [5] appeared. Rate Constant Calculation for Thermal Reactions: Methods and Applications, Edited by Herbert DaCosta and Maohong Fan. Ó 2012 John Wiley & Sons, Inc. Published 2012 by John Wiley & Sons, Inc. 3 4 OVERVIEW OF THERMOCHEMISTRY AND ITS APPLICATION TO REACTION KINETICS In 1936 was published The Thermochemistry of the Chemical Substances [6] where the authors Bichowsky and Rossini attempted to standardize the available data and published them at a common temperature of 18C (291K) and pressure of 1 atm.
    [Show full text]
  • Webpack Cheatsheet
    12/25/18, 655 PM Page 1 of 1 ! Edit Webpack cheatsheet — Proudly sponsored by — Airbrake.io Full-stack error tracking & analytics for Python developers. Try it Free! ethical ads via CodeFund This is a very basic “getting started with Webpack” guide for use with Webpack v3. This doesnʼt cover all features, but it should get you started in understanding the config file format. Basic config webpack.config.js module.exports = { context: __dirname, entry: 'src/app.js', output: { path: __dirname + '/public', filename: 'app.js' } } Terminal npm install --save-dev webpack webpack build webpack -- -p build production webpack -- --watch compile continuously This compiles src/app.js into public/app.js. (Note: you may need to use ./node_modules/.bin/webpack as a command if youʼre not invoking Webpack via npm scripts.) Multiple files webpack.config.js module.exports = { entry: { app: 'src/app.js', vendor: 'src/vendor.js' }, output: { path: __dirname + '/public', filename: '[name].js' } } This creates app.js and vendor.js. # Loaders Babel Terminal npm install --save-dev \ babel-loader \ babel-preset-env \ babel-preset-react webpack.config.js module.exports = { ··· module: { rules: [ { test: /\.js$/, exclude: /node_modules/, use: [ { loader: 'babel-loader' } ] } ] } } .babelrc { "presets": [ "env", "react" ] } Adds support for Babel. CSS Terminal npm install --save-dev \ css-loader \ style-loader webpack.config.js module.exports = { ··· module: { rules: [ { test: /\.css$/, exclude: /node_modules/, use: [ { loader: 'style-loader' }, { loader: 'css-loader'
    [Show full text]
  • Appendix a a List of the Program and Data Files on the Disk*
    Appendix A A List of the Program and Data Files on the Disk* 2dnrnr Simulates a IH COSY two-dimensional NMR plot (5.5). Abc Calculates principal moments of inertia for linear and non­ linear molecules (4.5). Acetate Calculates the pH in an acetate buffer (3.2). Anderko Solves the Anderko-Pitzer nonideal gas law (1.2). Aorbital Calculates and plots H atomic orbitals in two dimensions (4.3). Atpl Calculates and plots the apparent standard Gibbs energy I:irGo 1 for the ATP hydrolysis reaction at various pMg's and a specified pH and ionic strength (3.3). Atp2 Calculates and plots the apparent standard Gibbs energy I:irGo 1 for the ATP hydrolysis reaction at various pH's and a specified pMg and ionic strength (3.3). Beattie Solves the Beattie-Bridgeman nonideal gas law (1.2). Beyer Calculates and plots the density of states N(E) and the sum of states G(E) for a molecule's vibrational modes using the Beyer-Swinehart direct-count algorithm (11.4). Biochern Calculates and plots the apparent standard Gibbs energy I:irGo 1 for the F -+ M biochemical reaction at various pH's (3.3). Biokin Calculates and plots extracellular glucose and insulin con­ centrations as functions of time (10.4). Branch Calculates and plots H, 0, OH and 02 concentrations for the branching catalytic cycle that drives the 2H2 + 02 -+ 2H20 reaction (10.2). Brussels Calculates and plots concentrations of intermediates in the autocatalytic Brusselator model (11.5). Butler Calculates and plots the Butler-Volmer and Tafel equations relating electrode current and overpotential (11.6).
    [Show full text]
  • Pymol Modelling Workshop
    PyMOL Modelling Workshop My website: http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM442/ There you will find links to download the latest educational version of PyMOL as well as a link to my “Introduction to PyMOL”, which in turn has links to other people's PyMOL tutorials. Note also the PyMOL Wiki: http://pymolwiki.org. Structure files can be found by searching the Protein Data Bank (PDB) for structure: easy to remember website http://www.pdb.org. There is also the PDBe (PDB Europe, http://www.pdbe.org) that contains the same databank of structures, but with a different web interface for searching for structures and a different set of tools for analyzing structures. What is in a PDB file? Lots of information in the “header” (the section of the file preceding the actual atomic coordinates) as well as the coordinates for the atoms. When assessing a structure, one needs to take account of the resolution and R-factor, error estimates and missing residues. There is information about the sequence that was used to determine the structure with a sequence database reference. There is also information about the biological unit. In the case of crystal structures the biological unit may need to be generated by applying crystallographic symmetry operators, although there are web sites that also try to provide that information. (e.g. http://www.ebi.ac.uk/msd-srv/pisa/). Warning: One cannot blindly trust a crystal structure to be providing you with a completely accurate picture of reality. Reading the paper that describes the structure is a good start! Outline of PyMOL usage PyMOL is a very powerful, scriptable (customizable) tool for making publication-quality figures and performing analyses on structures.
    [Show full text]