DOCSLIB.ORG

Visual Molecular Dynamics a First Introduction to Scientific Visualization

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Visual Molecular Dynamics a First Introduction to Scientific Visualization Visual Molecular Dynamics A First Introduction to Scientific Visualization Geoffrey Gray VMD on CIRCE: On the lower bottom left of your screen, click on the window start-up menu. In the search box type “mstsc”. Click on “mstsc.exe”. On hostname type “circe.rc.usf.edu” Enter your login name and password at the prompts; this will open a new window. In this window on the menu bar select “Applications” (top left). Select “System Tools” at the bottom of the drag down menu. Select “Terminal”. In the terminal, type “module load apps/vmd/1.9”. Next type “vmd”; this will launch the program. Usage: During a simulation, a tremendous amount of data is generated. In general this is good, as it provides researchers with a large number of options for analysis. However, if you are unable to express this data in a meaningful way, then it is useless. One of the ways that computational scientists may try to interpret the results of their simulations is via the use of visualization software. There are many freely available programs available on the internet. Today we will use one of the most popular, Visual Molecular Dynamics (VMD) VMD allows the user to look at the crystal structure of a sample, or to watch a simulation by looking multiple frames (snapshots) of their simulation. We will look at these molecular “movies” in some of the later exercises. Right now, we will just look at single crystal structures. You might wonder where we could obtain a crystal structure of a protein. These structures are obtained experimentally and then downloaded as files to a large database known as the Protein Database (PDB). These PDB files are a common format for expressing molecular structures. In order to download our first file, go to the following website url: http://www.rcsb.org/pdb/home/home.do Today we will look at two different structures. First, type in the code 4OC7, a crystal structure of the retinoid X-receptor (RXR). It binds to DNA, regulating gene expression. The genes regulated by the RXR are involved in apoptosis (regulated cell death). Numerous diseases (such as cancer) occur when cell death fails to occur. Thus, by promoting the binding of the RXR to the gene, apoptosis is promoted, which had many therapeutic benefits. First load in the 4OC7 structure by going to File > New Molecule > Browse > Load. 2 Take a moment to look at the resulting crystal structure. Because it was obtained by X-ray crystal diffraction, the hydrogens do not show up. Why is this? Now that we have a crystal loaded, we can change the representation mode to display it in a way that may be more insightful to us. First let's change the representation by going to Graphics > Representations > Drawing Method > Licorice. 3 Notice this is very crowded, and it is difficult to really see the system in a helpful way. Thankfully, the makers of VMD have provided a variety of display options. Following the same procedure as before, change the drawing method to New Cartoon. This is a very pleasing way to display large proteins and gives structural information that otherwise is not available in methods that draw molecules as lines (e.g. lines, licorice, cpk, etc.). You will notice three different types of structures, twisting, flattened arrows, and coiled loops. These represent the secondary structure of α-helices, β-sheets, and loops. If you do not see them, that is okay, we can also change the coloring methods for the structure. To do this, under Representations, go to Coloring Method > Secondary Structure. 4 5 You will now see several different types of colors corresponding to four different structural elements. Purple corresponding to alpha helices, yellow for beta-sheets, white for turns, and cyan for regions. Notice how much more information we get from this representation, as opposed to the lines or the licorice. We now have experimental data on the structural features of our protein. Now that we have our protein expressed in a way that makes some sense to us, we can express individual portions of the protein differently. If any of your noticed, the protein was bound to a ligand. This ligand is not shown by New Cartoon, because it does not fall into any of the structural categories we have previously looked at. However, we can choose to show it in a different representation and include it in our image. Under Representations, press Create Rep. This will add a second representation, which we may then modify without disturbing the original. Highlight this second representation and in the Selected Atoms space type “not protein”. Once this is done, go to Drawing Method and choose Licorice, and then go to Coloring Method and choose Name. Now, compounds that are not proteins may be seen in conjunction with proteins. The selection option is a very powerful tool, and may be used to define a number of specific features. For example, create another representation by hitting Create Rep. Next type “resname ARG” as the selection. Now, consider if we wished to look at potential contacts between the ligand and the protein. To do this, we may select all atoms within a specified distance of the ligand (given in Å). Notice now how we have reduced the overwhelming image to only a few pertinent pieces of data. Load an MD Trajectory: In VMD perform the following: File > New Molecule. Browse > /shares/mri_workshop/visualization/md/conf.gro Load Browse > /shares/mri_workshop/visualization/md/md.trr Load This should load a trajectory for analysis. You should now see a “movie” playing on the screen. This shows the movement of the system through time. Once the movie has stopped, we can now perform analysis. First let’s align the trajectory. Extensions > Analysis > RMSD Trajectory In the lower right hand corner, hit “Add Active”. In the upper right corner hit “Align”, followed by “RMSD” (located directly to the left of “Align”). This will produce values for the RMSD next to the structure. Additionally it will align the trajectory, meaning that the overall structure will not rotate or translate (making it much easier to analyze). Now let’s perform some analysis. Following the previous example, select the protein and show as “New Cartoon”. Now, make a New Representation and show it as HBonds. This shows the hydrogen bonds formed in a system. Change the ColorID to red and the Line Thickness to 8. What do you see throughout the trajectory? Are any hydrogen bonds broken? Are any new hydrogen bonds formed? 6 While the methods used here are by no means quantitative, they give us unparalleled insight into what is occurring in our simulation and what sort of analysis we might perform. The techniques used today in VMD are in no way comprehensive. There are many more visualization schemes available. In addition, VMD can perform many basic calculations, and is easily modifiable to incorporate more complex calculations that a user may wish to perform. Despite the relatively few possibilities of this program that were used today, hopefully you now have a flavor of what VMD is capable. 7 Exercises: 1. One of the most studied proteins is Hemoglobin. Hemoglobin is known to exist in two states, R (relaxed) and T (tense). Both of these have been resolved in crystallographic studies. Download the files 1BBB and 1BZ0 (that’s a zero NOT and O), which are for the R state and the T state, respectively. Visualize both of these proteins separately and identify their subunits. How can we represent these structures in a useful way? How many subunits does Hemoglobin have? How could we identify them? 2. As previously mentioned, VMD can perform a number of numerical calculations. Here we will perform a simple overlay followed by an RMSD analysis. Load both of the structures and select Extensions > Analysis > RMSD Calculator. Change the selection to “protein” and click the Align button. This performs and overlay of the two structures, minimizing the RMSD between the two structures.Once they are aligned, click RMSD. What is the RMSD? Is this a lot? 3. In addition to RMSD, we can also calculate a Ramachandran Plot. Go to Extensions > Analysis > Ramachandran Plot. You will already see a standard plot for comparison obtained from a survey of many crystal structures (blue and green splotches). Go to molecule selection and look at both. How do the R and T states if Hemoglobin differ? How are they the same? 4. We can also click on the individual points to show the name and residue number of the amino acid, along with its ϕ and ψ angles. Which ones fall in the standard values? Which ones are outside of the standard values? 5. Now that you have identified the residues that are outside of the standard values, show these explicitly for both R and T state. How do they compare to each other? Why do you think these might be different? 6. In addition to a 2-dimensional display, the Ramachandran Plot may also be shown in 3- dimensions. Click on the Create 3-d Histogram. Does this show you anything that the 2- dimensional plot does not? Now show this plot for the other protein. Does comparing these plots give us additional information? Hint: to show the next protein, change your Molecule Selection and click on Create 3-d Histogram again. 8 VMD - quick guide: Download VMD: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD User guide: http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html To load in pdb file: File → New Molecule → Browse Click "Load" to load the file • Be sure to use the "Orthographic" projection: a more natural way to display the protein, by selecting: Display → Orthographic • To get rid of the axis: select Display → Axes → Off To rotate: press "r" and move mouse To translate: press "t" and move mouse To recenter: press "c" and use mouse to select new center of rotation To make bigger/smaller: press "s" (scale) and move mouse To measure distances: press 2 and select 2 atoms with the mouse.
Load more

Recommended publications
  • Mercury 2.4 User Guide and Tutorials 2011 CSDS Release
    Mercury 2.4 User Guide and Tutorials 2011 CSDS Release Copyright © 2010 The Cambridge Crystallographic Data Centre Registered Charity No 800579 Conditions of Use The Cambridge Structural Database System (CSD System) comprising all or some of the following: ConQuest, Quest, PreQuest, Mercury, (Mercury CSD and Materials module of Mercury), VISTA, Mogul, IsoStar, SuperStar, web accessible CSD tools and services, WebCSD, CSD Java sketcher, CSD data file, CSD-UNITY, CSD-MDL, CSD-SDfile, CSD data updates, sub files derived from the foregoing data files, documentation and command procedures (each individually a Component) is a database and copyright work belonging to the Cambridge Crystallographic Data Centre (CCDC) and its licensors and all rights are protected. Use of the CSD System is permitted solely in accordance with a valid Licence of Access Agreement and all Components included are proprietary. When a Component is supplied independently of the CSD System its use is subject to the conditions of the separate licence. All persons accessing the CSD System or its Components should make themselves aware of the conditions contained in the Licence of Access Agreement or the relevant licence. In particular: • The CSD System and its Components are licensed subject to a time limit for use by a specified organisation at a specified location. • The CSD System and its Components are to be treated as confidential and may NOT be disclosed or re- distributed in any form, in whole or in part, to any third party. • Software or data derived from or developed using the CSD System may not be distributed without prior written approval of the CCDC.
    [Show 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.) 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]
  • Instructions on Making Pdf Files Containing 3D
    Detailed Instructions for Creating an Embedded Virtual 3-D Image of a Molecule Creating the documents with embedded virtual three-dimensional images may be done fairly easily by repeating the following procedures. Once you have embedded your first image, the use of that image is limited only by your imagination. The following instructions are written in extreme detail with annotated screen shots of the four programs you will use throughout for clarification. Once you are familiar with the procedure embedding a structure of interest should take less than 20 min., limited only by the speed with which you can click a mouse. In practice most of our embedded 3-D images have been created by our undergraduate student collaborators. Step 1. Creating a 2-D image in ChemSketch Using ACD ChemSketch 11.0 Freeware (http://www.acdlabs.com/download/chemsk_download.html ) a two dimensional structure may be drawn as per your specific need (see Figure 1). Once the molecule is drawn, optimized it by clicking the 3-D optimization button then save as an MDL molfile (*.mol). Figure 1: A screen shot of acetone drawn with ChemSketch after 3-D optimization. Step 2. Converting the *.mol file to a *.pdb file using Open Babel The file can now be converted from a .mol file to a .pdb file, Protein Data Bank format, to be properly accessed with the Adobe Acrobat 3D Toolkit 8.1.0. The file conversion is done using Open Babel Graphical User Interface v2.2.0 (openbabel.sourceforge.net) under default settings. Step by step instructions: A.
    [Show full text]
  • Getting Started in Jmol
    Getting Started in Jmol Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingResources/jmol/jmolTraining/started.html Introduction Physical models of proteins are powerful tools that can be used synergistically with computer visualizations to explore protein structure and function. Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own! At the MSOE Center for BioMolecular Modeling we use the molecular visualization program Jmol to explore protein and molecular structures in fully interactive 3-dimensional displays. Jmol a free, open source molecular visualization program used by students, educators and researchers internationally. The Jmol Training Guide from the MSOE Center for BioMolecular Modeling will provide the tools needed to create molecular renderings, physical models using 3-D printing technologies, as well as Jmol animations for online tutorials or electronic posters. Examples of Proteins in Jmol Jmol allows users to rotate proteins and molecular structures in a fully interactive 3-dimensional display. Some sample proteins designed with Jmol are shown to the right. Hemoglobin Proteins Insulin Proteins Green Fluorescent safely carry oxygen in the help regulate sugar in Proteins create blood. the bloodstream. bioluminescence in animals like jellyfish. Downloading Jmol Jmol Can be Used in Two Ways: 1. As an independent program on a desktop - Jmol can be downloaded to run on your desktop like any other program. It uses a Java platform and therefore functions equally well in a PC or Mac environment. 2. As a web application - Jmol has a web-based version (oftern refered to as "JSmol") that runs on a JavaScript platform and therefore functions equally well on all HTML5 compatible browsers such as Firefox, Internet Explorer, Safari and Chrome.
    [Show full text]
  • Chemdoodle Web Components: HTML5 Toolkit for Chemical Graphics, Interfaces, and Informatics Melanie C Burger1,2*
    Burger. J Cheminform (2015) 7:35 DOI 10.1186/s13321-015-0085-3 REVIEW Open Access ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics Melanie C Burger1,2* Abstract ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses <canvas> and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochem- istry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses. Keywords: ChemDoodle Web Components, Chemical graphics, Animations, Cheminformatics, HTML5, Canvas, JavaScript, WebGL, Structure editor, Structure query Introduction Mobile browsers did support HTML5, which opened How we communicate chemical information is increas- the door to web applications built with only HTML, ingly technology driven. Learning management systems, CSS and JavaScript (JS), such as the ChemDoodle Web virtual classrooms and MOOCs are a few examples where Components. chemistry educators need forward compatible tools for digital natives. Companies that implement emerg- Review ing web technologies can find efficiencies and benefit The ChemDoodle Web Components technology stack from competitive advantages. The first chemical graph- and features ics toolkit for the web, MDL Chime, was introduced in The ChemDoodle Web Components library, released in 1996 [1]. Based on the molecular visualization program 2009, is the first chemistry toolkit for structure viewing RasMol, Chime was developed as a plugin for Netscape and editing that is originally built using only web stand- and later for Internet Explorer and Firefox.
    [Show full text]
  • How to Modify LAMMPS: from the Prospective of a Particle Method Researcher
    chemengineering Article How to Modify LAMMPS: From the Prospective of a Particle Method Researcher Andrea Albano 1,* , Eve le Guillou 2, Antoine Danzé 2, Irene Moulitsas 2 , Iwan H. Sahputra 1,3, Amin Rahmat 1, Carlos Alberto Duque-Daza 1,4, Xiaocheng Shang 5 , Khai Ching Ng 6, Mostapha Ariane 7 and Alessio Alexiadis 1,* 1 School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK; [email protected] (I.H.S.); [email protected] (A.R.); [email protected] (C.A.D.-D.) 2 Centre for Computational Engineering Sciences, Cranfield University, Bedford MK43 0AL, UK; Eve.M.Le-Guillou@cranfield.ac.uk (E.l.G.); A.Danze@cranfield.ac.uk (A.D.); i.moulitsas@cranfield.ac.uk (I.M.) 3 Industrial Engineering Department, Petra Christian University, Surabaya 60236, Indonesia 4 Department of Mechanical and Mechatronic Engineering, Universidad Nacional de Colombia, Bogotá 111321, Colombia 5 School of Mathematics, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; [email protected] 6 Department of Mechanical, Materials and Manufacturing Engineering, University of Nottingham Malaysia, Jalan Broga, Semenyih 43500, Malaysia; [email protected] 7 Department of Materials and Engineering, Sayens-University of Burgundy, 21000 Dijon, France; [email protected] * Correspondence: [email protected] or [email protected] (A.A.); [email protected] (A.A.) Citation: Albano, A.; le Guillou, E.; Danzé, A.; Moulitsas, I.; Sahputra, Abstract: LAMMPS is a powerful simulator originally developed for molecular dynamics that, today, I.H.; Rahmat, A.; Duque-Daza, C.A.; also accounts for other particle-based algorithms such as DEM, SPH, or Peridynamics.
    [Show full text]
  • Preparing and Analyzing Large Molecular Simulations With
    Preparing and Analyzing Large Molecular Simulations with VMD John Stone, Senior Research Programmer NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign VMD Tutorials Home Page • http://www.ks.uiuc.edu/Training/Tutorials/ – Main VMD tutorial – VMD images and movies tutorial – QwikMD simulation preparation and analysis plugin – Structure check – VMD quantum chemistry visualization tutorial – Visualization and analysis of CPMD data with VMD – Parameterizing small molecules using ffTK Overview • Introduction • Data model • Visualization • Scripting and analytical features • Trajectory analysis and visualization • High fidelity ray tracing • Plugins and user-extensibility • Large system analysis and visualization VMD – “Visual Molecular Dynamics” • 100,000 active users worldwide • Visualization and analysis of: – Molecular dynamics simulations – Lattice cell simulations – Quantum chemistry calculations – Cryo-EM densities, volumetric data • User extensible scripting and plugins • http://www.ks.uiuc.edu/Research/vmd/ Cell-Scale Modeling MD Simulation VMD – “Visual Molecular Dynamics” • Unique capabilities: • Visualization and analysis of: – Trajectories are fundamental to VMD – Molecular dynamics simulations – Support for very large systems, – “Particle” systems and whole cells now reaching billions of particles – Cryo-EM densities, volumetric data – Extensive GPU acceleration – Quantum chemistry calculations – Parallel analysis/visualization with MPI – Sequence information MD Simulations Cell-Scale
    [Show full text]
  • 2 – 3 Wall Ball Only a Jelly Ball May Be Used for This Game. 1. No Games
    One Fly Up Switch 5. After one bounce, receiving player hits the ball 1 – 2 – 3 Wall Ball Use a soccer ball only. Played in Four Square court. underhand to any another square. No “claws” (one hand Only a jelly ball may be used for this game. 1. The kicker drop kicks the ball. on top and one hand on the bottom of the ball). 2. Whoever catches the ball is the next kicker. 1. Five players play at a time, one in each corner and one 6. Players may use 1 or 2 hands, as long as it is underhand. 1. No games allowed that aim the ball at a student standing 3. Kicker gets 4 kicks and if the ball is not caught, s/he in the middle of the court. 7. Players may step out of bounds to play a ball that has against the wall. picks the next kicker. bounced in their square, but s/he may not go into 2. No more than three players in a court at one time. 2. When the middle person shouts “Switch!” in his/her another player’s square. 3. First person to court is server and number 1. No “first loudest voice, each person moves to a new corner. Knock Out 8. When one player is out, the next child in line enters at serves”. 3. The person without a corner is out and goes to the end Use 2 basketballs only for this game. the D square, and the others rotate. 4. Ball may be hit with fist, open palm, or interlocked of the line.
    [Show full text]
  • Chem3d 17.0 User Guide Chem3d 17.0
    Chem3D 17.0 User Guide Chem3D 17.0 Table of Contents Recent Additions viii Chapter 1: About Chem3D 1 Additional computational engines 1 Serial numbers and technical support 3 About Chem3D Tutorials 3 Chapter 2: Chem3D Basics 5 Getting around 5 User interface preferences 9 Background settings 10 Sample files 10 Saving to Dropbox 10 Chapter 3: Basic Model Building 12 Default settings 12 Selecting a display mode 12 Using bond tools 13 Using the ChemDraw panel 15 Using other 2D drawing packages 15 Building from text 16 Adding fragments 18 Selecting atoms and bonds 18 Atom charges 21 Object position 23 Substructures 24 Refining models 27 Copying and printing 29 Finding structures online 32 Chapter 4: Displaying Models 35 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. ii Chem3D 17.0 Display modes 35 Atom and bond size 37 Displaying dot surfaces 38 Serial numbers 38 Displaying atoms 39 Atom symbols 40 Rotating models 41 Atom and bond properties 44 Showing hydrogen bonds 45 Hydrogens and lone pairs 46 Translating models 47 Scaling models 47 Aligning models 47 Applying color 49 Model Explorer 52 Measuring molecules 59 Comparing models by overlay 62 Molecular surfaces 63 Using stereo pairs 72 Stereo enhancement 72 Setting view focus 73 Chapter 5: Building Advanced Models 74 Dummy bonds and dummy atoms 74 Substructures 75 Bonding by proximity 78 Setting measurements 78 Atom and building types 81 Stereochemistry 85 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. iii Chem3D 17.0 Building with Cartesian
    [Show full text]
  • Open Source Molecular Modeling
    Accepted Manuscript Title: Open Source Molecular Modeling Author: Somayeh Pirhadi Jocelyn Sunseri David Ryan Koes PII: S1093-3263(16)30118-8 DOI: http://dx.doi.org/doi:10.1016/j.jmgm.2016.07.008 Reference: JMG 6730 To appear in: Journal of Molecular Graphics and Modelling Received date: 4-5-2016 Accepted date: 25-7-2016 Please cite this article as: Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes, Open Source Molecular Modeling, <![CDATA[Journal of Molecular Graphics and Modelling]]> (2016), http://dx.doi.org/10.1016/j.jmgm.2016.07.008 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Open Source Molecular Modeling Somayeh Pirhadia, Jocelyn Sunseria, David Ryan Koesa,∗ aDepartment of Computational and Systems Biology, University of Pittsburgh Abstract The success of molecular modeling and computational chemistry efforts are, by definition, de- pendent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. 1. Introduction What is Open Source? Free and open source software (FOSS) is software that is both considered \free software," as defined by the Free Software Foundation (http://fsf.org) and \open source," as defined by the Open Source Initiative (http://opensource.org).
    [Show full text]
  • Molecular Modeling with Pymol
    Molecular Modeling with PyMOL PyMOL software is distributed under a license that permits use by Professor Nowick and his students for research and teaching purposes. Students of Professor Nowick may contact him for a link to download PyMOL. PyMOL can perform molecular mechanics calculations to generate realistic molecular models of molecules with common types of atoms and functional groups. Molecular mechanics uses a force field to calculate the steric energy of the molecule and then adjusts the conformation of the molecule to minimize the steric energy. A force field is set of parameters for the bond lengths, angles, torsional parameters, electrostatic properties, van der Waals interactions, etc. PyMOL uses the Merck Molecular Force Field (MMFF), which accurately accommodates a variety of atom types and functional groups. The conformation generated by molecular mechanics is a local minimum. A local minimum is a conformation at the bottom of an energy well (i.e., a conformer). It is not necessarily the lowest energy conformer (i.e., the global minimum). If you start near gauche butane, you will generate gauche butane as a local minimum; if you start near anti butane, you will generate anti butane as a local minimum that is also the global minimum. If you start with a boatlike conformation of cyclohexane, you will end up with a twist-boat conformer; if you start with a chairlike conformation of cyclohexane, you will end up with a chair conformer. The lowest-energy conformer (global minimum) many be identified by various strategies. With simple molecules and small ring sizes, this is often best done by manually adjusting the structure and re-minimizing the structure.
    [Show full text]
  • Visualisations Generating a Graph Set View
    1 Table of Contents Example 1. Generating Structure Views ............................................................................. 2 Generating a Simple Molecular View ............................................................................. 2 Generating Ellipsoid and Polyhedral Views .................................................................... 4 Generating a Packing Diagram ....................................................................................... 6 Displaying Intermolecular Contacts ............................................................................... 7 Visualisations Generating a Graph Set View ......................................................................................... 8 Example 2. Generating Images and 3D Print Files.............................................................. 9 High-resolution images .................................................................................................. 9 Version 1.2 – October 2019 Generating Rotating Images. ........................................................................................ 10 Teaching Subset v5.40 Generating a 3D Print Model File ................................................................................. 11 2 Example 1. Generating Structure Views In order to communicate science effectively, researchers must be able to provide clear images of structural models for inclusion in manuscripts and presentations. The program Mercury contains many features which can assist in the production of high-quality, high-resolution
    [Show full text]