StarBiochem User Manual
Contents
1. PDB Information K Changing visibility of side chains and backbones 1 Click on Structure to open the tabbed list of controls 2 Navigate between the tabs to select and unselect primary secondary tertiary or quaternary structures 3 Inthe View Controls panel change the visibility of corresponding atoms by manipulating the Sidechain or Backbone sliders or by entering a number between 0 and 1 in the boxes to the right of the sliders 4 Check the Selected Residues Use Transparency box so that manipulating the sliders affects only the selected atoms A ON AN StarBiochem 3D9S File View Help Structure V View Controls gt Secondary Structures Use V Transparency Unselected OQO 0 11 Selected 1 Selected Residues Use Transparency Backbone O 0 Sidechain 1 Atoms M Draw C Fill space Bonds M Draw Selection Controls V PDB Tree PDB Information V Measurement Tools lt2. Atoms M Draw M Fill space Bonds M Draw sh A A wi es 2 a Ghow Ail Ji a 6 vi S Cae Selection Controls Measurement Tools PDB Tree QIQ PDB Information The default coloring scheme for atoms is as follows e Carbon C atoms grey spheres e Oxygen O atoms red spheres e Nitrogen N atoms blue spheres e Sulfur S atoms yellow spheres e Standard bonds grey line segments e Peptide bonds blue line segments Note StarBiochem does not display hydrogen atoms or water molecules contained in the PDB files Displaying molecular structures The primary structure of a protein lists the amino acids that make up a protein s sequence or the nucleotides that make up a DNA segment but does not describe their corresponding shape The secondary structure of a protein refers to how stretches of amino acids within a protein chain are arranged in space in characteristic patterns such as helices sheets and coils The tertiary structure describes the folded shape of a protein chain and is determined by characteristic properties of the amino acid residues such as acidic basic polar and non polar The quaternary structure indicates the relationship between the chains of a molecule Note for DNA segments that are crystallized with DNA binding proteins only the primary structure of the DNA segment is shown Displaying primary structures 1 Click on the Structure 2 Select
3. Cancel e the Bundled Samples folder click on the desired PDB file and then click Open e the Desktop click on PDB file within the Desktop folder and then click Open e the PDB database via PDB RCBS Search in the Search Keywords enter the PDB ID or type the name of the protein Click on the Search results file within the PDB RCBS Search tool Choose the desired PDB file and click Open a0 0 Open Look In GH Search results for aquaporin M Ee fel c3 E 2B6P 209E 3D95 3D95 2c32 209F HUMAN AQUAPORIN 0 ome 5 AOPS 2057 209G 7E S HIGH RESOLUTI TS 2evu 3CLL we ON X RAY STRUCTURE 2F28 3CNs R HORSEFIELD K N 7 3 2090 4 3CN6 SE lt gt 4 il gt FileName 3D95 Files of Type All Files M Open Cancel Upon opening PDB file in StarBiochem you will see a 3D model of the protein in the viewer StarBiochem 3D9S _ File View Help Structure View Controls Selection Controls Measurement Tools PDB Tree PDB Information Manipulating the default view To rotate Windows left click and drag the mouse Mac click and drag the mouse To move up down right left Windows right click and drag the mouse Mac apple click and drag the mouse To zoom Windows Alt left click and drag the mouse Mac option click and drag the mouse Note sometimes you may need to zoom
4. StarBiochem User Manual Learn how use StarBiochem Contents Opening StarBiochem Loading a protein structure Manipulating the default view Visualizing atoms and bonds Displaying molecular structures Selecting atoms and structures oOo won un A W WW Manipulating molecule visibility Welcome to StarBiochem StarBiochem is a protein 3D viewer StarBiochem runs on standard Linux Windows and Mac computers Opening StarBiochem To get started with StarBiochem 1 Navigate to http web mit edu star biochem 2 Click on the Start button to launch the StarBiochem application 3 Click Trust when a prompt appears asking if you trust the certificate This is the view you will see when you open StarBiochem nano StarBiochem File View Help View Controls Selection Controls C O n t ro S Measurement Tools PDB Tree PDB Information Loading a protein structure StarBiochem enables the visualization of molecules encoded within Protein Data Bank PDB files PDB files are named by a four character ID such as 1GXX To open a PDB file 1 Click on File gt Open Import 2 Inthe Look In pull down menu choose a PDB file from one of the following sources SN AS AN Open Look In ca Bundled Samples x l fel BB 1A3N f 6PFK 1DX8 1GXX 1H6l 4 1PFK Package has 10 objects File Name Files of Type All Files Open
5. e Tertiary tab in the Structure panel 2 Check a property box e g Basic Acidic etc to color different types of residues in the viewer 3 Uncheck the property box to return to the default coloring scheme Displaying quaternary structures 1 Click on the Quaternary tab in the Structure panel 2 Check the Chain box to color all atoms according to the chain to which they belong AAD StarBiochem 3D9S File View Help Structure A 4 Tertiary Quaternary Color by M Chain View Controls NA Selection Controls Measurement Tools lollo 3 Uncheck the Chain box to return to the original color scheme Selecting atoms and structures In addition to being able to select structural elements within the Structure controls StarBiochem allows for selection of individual structural elements by selecting the type of element and then clicking on the actual element within the structure Selecting individual structural elements 1 Click on Selection Controls to open the panel for selecting elements of the molecule 2 Inthe Select by groups click on the button corresponding to the type of structural element you want to select Selection Controls a Select by mouse click NONE Atom Y Residue Chain Helix Sheet gt Coil Select All I None Select residue by type _ ALA Alanine _ ARG Arganine 3 Inthe viewer click on
6. out to see the entire molecule after it first loads Visualizing atoms and bonds The default view of a molecule is the ball and stick mode where the bonds have been drawn but not the atoms To visualize hide atoms or bonds in the ball and stick view mode 1 Click the View Controls panel 2 Check the Draw checkbox under the Atoms or Bonds box to turn the corresponding elements or uncheck the box to turn them off ANG StarBiochem 3D9S File View Help Structure Vv View Controls gt Secondary Structures Use v Transparency Unselected 1 Selected 1 Selected Residues Use v Transparency Backbone 1 Sidechain 1 Atoms M Draw C Fill space Bonds M Draw Show All Show All Selection Controls Y Measurement Tools C PDB Tree PDB Information To change the default ball and stick view to the space fill view 1 Click the View Controls panel 2 Check the Fill space checkbox under the Atoms box to display atoms in the space filled mode uncheck the box to display them in default ball and stick mode 000 StarBiochem 3D9S File View Help Structure DG View Controls Secondary Structures Use M Transparency Unselected 1 Selected 1 Selected Residues Use M Transparency Backbone 1 Sidechain 1
7. the Primary tab to display the primary structure a numbered list of amino acids Structure Primary Secondary Tertiary Ser 1 lys 2 lys 3 Glu_4 r val 5 Cys_6 Ser 7 Val 8 Ala 9 Phe_10 Leu 11 Lys 12 Ala 13 Val 14 Phe 15 Ala 16 3 If necessary scroll down through multiple numbered lists of amino acids every list corresponds to a different protein chain discussed later in the molecule and is color coded accordingly Left click on a list entry to select a particular amino acid in the viewer To select multiple amino acids hold down Ctrl while clicking on them Displaying secondary structures 1 Click on the Secondary tab in the Structure panel 2 Select Helix Sheet or Coil respectively to display secondary structures in the standard ribbon format ribbon like strips in the shape of helices sheets or coils AAD StarBiochem 3D9S File View Help Structure A f Primary Secondary Tertiary gt Track Selection Show Ribbons C All Ribbons M Helices C Sheets O Coils Helix Selection J Go Noon 8 a oo w N E f wo An w Coil Selection a v View Controls Selection Controls Measurement Tools Q 3 You can select individual helices sheets or coils by clicking on the individual selection checkboxes for each of these secondary structures Displaying tertiary structures 1 Click on th
8. the actual structural element to select the type of object indicated in the Select by boxes 4 Toselect multiple atoms sets of atoms hold down Ctr while clicking on these elements To unselect structural elements hold down Ctr while clicking on the selected elements Manipulating molecule visibility StarBiochem enables the user to focus on specific elements of the molecule by controlling the transparency of selected or unselected atoms side chains and backbones Changing visibility of selected and unselected atoms 1 Click on Structure to open the tabbed list of controls 2 Navigate between the tabs to select and unselect primary secondary tertiary or quaternary structures 3 Click on the View Controls bar to open the panel Change the visibility of corresponding atoms by manipulating the Unselected or Selected sliders or by entering a number between 0 and 1 in the boxes to the right of the sliders 5 Check the Secondary Structures Use Transparency box so that manipulating the sliders affects also the transparency of any visible secondary structures AAD StarBiochem 3D9S File View Help View Controls gt Secondary Structures Use Transparency Unselected Q 0 15 Selected 1 Selected Residues Use v Transparency Backbone 1 Sidechain oe 1 Atoms M Draw C Fill space Bonds M Draw Show All Selection Controls V Measurement Tools PDB Tree V
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