DEEP VIEW Tutorial - Introduction to Program A Bit about DEEP VIEW
Contents
1. Bar in PART IV Tool Bar Buttons First 4 buttons starting from left to right Zoom Center arrows pointing in toward a residue This automatically zooms to fill the screen with whatever is currently on display Use this function when ever a view becomes awkward Translate hand This translates your model when you click and move your mouse over your model Zoom boxes This zooms your model Rotate circular arrow This rotates your model e Tip Pressing TAB Cycles through the translate zoom and rotate functions from left to right O Pressing SHIFT TAB Cycles through the translate zoom and rotate functions from right to left PART III The Control Panel The control Panel is very important It lists all the groups in your model and lets you select display or hide parts of the model It may seem overwhelming at first but as with RASMOL the more you play the easier it will all come Raw i e Column Headings From Left to Right Page 4 of 11 Deep View Tutorial Introduction to Program e Far most left which is blank in this case When a protein contains more than one chain the letter designation Usually A amp B for each chain appears here e s amp h to the left of the group column secondary structure sheet and helix respectively e Group lists the residue and hetero group names and numbers e Show displays the backbone of an individual or selected residues e S2. htm e Download PDB files PDB site http www rcsb org pdb DEEP VIEW User Guide and Help e User Guide http us expasy org spdbv text main htm e Help directions http www usm maine edu 7Erhodes OHelp GetSPdbV html Additional DEEP VIEW Tutorials e Gale Rhodes U Southern Maine http www usm maine edu rhodes SPVTut index html MOST RECOMMENDED e From DEEP VIEW Homepage Expasy http us expasy org spdbv text tutorial htm e U Arizona formally used in Graduate course 585 Biological Structure http www biochem arizona edu classes bioc585 protnuc example example htm Tutorial Exercise This exercise is designed to teach you the basics of molecular graphics display using the program DEEP VIEW If you have any questions please ask We will be using the enzyme lysozyme in complex with the trisaccharide inhibitor tri N acetylglucosamine or tri NAG Atomic coordinates contained in the Protein Data Bank have a pdb code of 1HEW pdb Tutorial Exercise Objectives e Start and download structures into DEEP VIEW e Understand the Windows of DEEP VIEW e Become familiar with the Control Panel Page 2 of 11 Deep View Tutorial Introduction to Program e Become familiar with the Tool Bar e Practice keyboard modifiers Part I Getting Started and Knowing the Various Windows of DEEP VIEW e Creating a DEEP VIEW folder e Obtaining the PDB file 1HEW pdb e Starting DEEP VIEW e Opening a PDB structure e Ope
3. Deep View Tutorial Introduction to Program DEEP VIEW Tutorial Introduction to Program Created by Angela M Amoia 09 21 03 Adapted from a tutorial by Gale Rhodes Updated by Matt Cordes 09 26 05 Last Updated by Angela M Amoia 08 06 Lesson Date 09 20 06 W A Bit about DEEP VIEW The following program DEEP VIEW version 3 7 formally called SWISS PDB VIEWER is used to translate a PDB file containing detailed molecular structure information into a picture The PDB files from published structures from both nuclear magnetic resonance spectroscopy and x ray crystallography are available at the Brookhaven Protein Data Bank http www rcsb org pdb index html This shareware free software is a more robust visualization program than RASMOL and is commonly used by many structural biologists Although the rendering is not as nice as in RASMOL it provides a number of powerful tools for displaying and manipulating macromolecular structure that RASMOL can not The user can display multiple structures display electron density or electrostatic maps display crystal symmetry useful for displaying an entire molecule create mutants perform sequence alignments superimpose related molecules perform energy minimization s and so on If you are interested in structural biology research you should learn how to use this program thoroughly For more information on what DEEP VIEW can do please see the introduction to Gale Rhodes tutorial as wel
4. T IID e Color Provides many different ways to color a model Color is not trivial It can reveal structural chemical and comparative features It is to note that the same operations in this menu can also be done through the Control Panel i e the last two raws to far right o lst Choose an act on BB amp SC BB only ect Backbone Sidechains Oo O00 0 0 O O Backbone Sidechains Ribbon Label Surface o 2nd Choose a by CPK carbon gray nitrogen blue oxygen red Type basic blue acidic red nonpolar gray yellow polar uncharged Page 9 of 11 Deep View Tutorial Introduction to Program Note aromatics are included into one of the above categories Ex Tyr is yellow thus polar and uncharged e Secondary Structure alpha helices red beta sheets blue coil gray e Accessibility The darker the color the less accessible to solvent Preferences Sets how you want to the program to perform In other words you can customize tools to your liking I suggest not changing anything for this class and use the programs default preferences Swiss Model Creates homology models This is beyond the scope of this class thus ignore this menu Window Please see PART I for details Help Provides help files for the Tool Bar Control Panel Layer Info Alignment and Ramachandran Plot Windows Note These help files can also be found by clicking the red i
5. al Introduction to Program 4 Select and display only the residues whose sidechains carry positive charge i e basic residues o Where are these residues located o What color are they o Name two of these residues 5 Select and display only the histidine residues and their side chains o How many histidines are present in lysozyme o When colored by type what color are histidines 6 How many disulfide bonds are present in this model What are the residue names and numbers involved in these disulfide bonds 7 What is the approximate length of a disulfide bond 8 What is the approximate length of a hydrogen bond Hint you first have to Compute H bonds from the Tools menu pulldown then measure the distance 9 Name two residues within 6A of the heteroatom NAG Extra Problem 10 Make a model in which lysozyme is shown only as a ribbon colored by secondary structure and tri NAG is shown in normal CPK colors with a dotted van der Waals surface e What are the steps you used to accomplish this view Page 11 of 11
6. d and thus turns red Press Enter to display the chain e Click on any h in the second column This selects all residues in that helix Press Enter to display the helix e Click on another h or s This changes your selection Press Enter to display Page 7 of 11 Deep View Tutorial Introduction to Program PART IV The Tool Bar The Tool Bar allows you to perform a variety of actions We will not be able to go through all the icons or pulldown menus today so I suggest playing on your own Instead we will have a brief overview of the icons not mentioned in PART II and of some of the more basic and or useful operations in the pulldown menus Buttons From Left to Right To use simply click on the button and follow the directions which appear below it in red e Zoom Center arrows pointing in toward a residue This automatically zooms to fill the screen with whatever is currently on display Use this function when ever a view becomes awkward Manipulative e Translate hand This translates your model when you click and move your mouse over your model e Zoom boxes This zooms your model e Rotate circular arrow This rotates your model Most Commonly Used Tools e Distance between two atoms e Angle between three atoms e Dihedral angles By default gives a measure of omega phi and psi angles of the picked amino acid e Atom Identification e Display Undisplay selected groups in a certain radius e Ce
7. es are now labeled e Click on the raw heading picture of dots This shows a dotted van der walls or accessible surface on all selected residues depending on which is activated e Click on the raw heading word ribn This draws a smooth stranded cartoon of the selected backbone e Remove all labels surface and ribbon Try both of these ways o SHIFT Click simultaneously on a checkmark in the respective raw OR o CTRL SHIFT Click on the raw heading Note To add all labels surface and ribbon again simply use the above in an empty space in the respective raw e Add but not select residues 16 24 to your model Click from residue 16 24 in the show raw Notice checks appear however they do not turn red This means that residues 25 36 are selected and shown while residues 16 24 are shown but NOT selected e Press on the numeric key pad This toggles on and off the selected groups without affecting the other groups End with residues 16 36 displayed e Press Enter Notice that residues 16 24 disappear because they were not selected e Select and display residues 13 and 19 in addition to what is already selected o CTRL Click on residues 13 and 19 in the group raw They should turn red o Press Enter to add them to the display o Click on the raw heading side to turn on their sidechains e Click anywhere in the far most left blank raw Notice the entire chain in this case the entire model has been selecte
8. ide displays the sidechains of an individual or selected residues e Labl Labels individual or selected residues e Dots displays a dotted van der Waals or accessible surface of an individual or selected residues depending on which is activated e Ribn Stands for Ribbon draws a smooth stranded cartoon of the selected backbone e Col Shows the color of each residue when colored e Far most right Chooses what you want to color ex backbone sidechains backbone only label ect Tips and keyboard modifiers When click on a group name e SHIFT acts meaning selects deselects on all groups e CTRL acts only on selection without affecting other groups e SHIFT CTRL deselects e Right Click centers a group or select groups belonging to the same secondary structure e In general to select a group of residues in a row o Click and drag on those residues in the group column OR Page 5 of 11 Deep View Tutorial Introduction to Program o Click on the first residue and SHIFT Click on the last residue of interest When click on a checkmark raw In general clicking in the checkmark raws next to a group acts on individual residues groups In general clicking on a heading at the top of the raw acts on all selected i e red residues SHIFT acts meaning checks unchecked on the whole raw SHIFT CTRL acts on the whole raw of each layer Additional Enter adds selected groups and removes
9. l as the ExPASy Expert Protein Analysis System Molecular Biology Server Both web addresses can be found below DEEP VIEW as an Analytical Tool e Build models from scratch e Find H bonds within proteins and between proteins and ligands e Examine e density maps from crystallographic structure determination e Judge quality of maps and models e View several proteins simultaneously e Superimpose structures to compare structure and sequence e Carry out energy minimization e Creates homology models with SWISS MODEL Computing Platforms for running DEEP VIEW DEEP VIEW runs best on a Macintosh PowerPC a UNIX computer e g an SGI or a Pentium based computer running Windows or NT Other computers can be used but tend to be slow In addition to Page 1 of 11 Deep View Tutorial Introduction to Program the computers available for this course suitable computers can be found in the CCIT computing labs and the Biology Learning Center e CCIT http www ccit arizona edu e Biology Learning Center BLC http www blc arizona edu Downloading DEEP VIEW and PDB files To run DEEP VIEW you must obtain the program DEEP VIEW 3 7 already downloaded on the Biochemistry Lab computers and a Protein Data Bank PDB file which contains the coordinates for the structure to be viewed e DEEP VIEW Umbrella Page ExPASy http www expasy ch spdbv mainpage html e Download DEEP VIEW version 3 7 http us expasy org spdbv text disclaim
10. n each window Also provided here is a web or local based copy of the user manual Exercise Now Let s play with these a bit Since many of the menus and buttons are relatively intuitive there will be less guidance on getting the end result and more questions asked Please put answers on a separate piece of paper you will be asked to hand these in the Wednesday after the exam We will concentrate on the Select Display and Color pulldown menus first l Select and display the whole molecule and color it CPK Go to the Select pulldown menu then to all To display residues press Enter o Again what were the steps you used to accomplish this Select and display accessible residues with a cut off of 30 Go to the Select pulldown menu then to accessible aa Enter a cut off of 30 and then press OK To display only these residues press Enter o Where are most of these residues located Hint color by accessibility o What type of residues are they Hint color by type o Name two of these residues Select and display all residues involved in beta strands Notice the characteristic pattern of hydrogen bonds in the strands Note To turn on H bonds go to the Tools menu pulldown and then choose Compute H bonds To turn off H bonds go to the Display menu pulldown and then uncheck Show H bonds o How many strands are shown o Are they close in the primary amino acid sequence Page 10 of 11 Deep View Tutori
11. ning Various Windows Control Panel Alignment Layers Infos Ramachandran Plot e Create a DEEP VIEW folder in your directory Unlike RASMOL you do not need to save everything dealing with DEEP VIEW in this folder to have the program work properly However for organizational purposes I highly suggest that you keep everything dealing with DEEP VIEW in this folder e Obtain the PDB file 1HEW pdb This can be done 1 of 2 ways 1 On the course website under Computer Section Shared PDB s and RASMOL Scripts 2 Go to the PDB and retrieve the coordinate file for lysozyme in complex with tri NAG that has the name 1HEW e Start DEEP VIEW Double click on the DEEP VIEW icon on your desktop A window that has credits will pop up Close this window You will now see a window with menu pull downs as well as picture icons This is called the Tool Bar and will be referred to as such from this point on e Opening a PDB structure Go to the File pulldown menu at the top of the Tool Bar window Scroll to Open PDB File Scroll to your Deep View folder and open 1HEW pdb The protein should appear as a wireframe model in a black window which is labeled with the name of the PDB file This is called the in the Display window and will be referred to as such from this point on Note Unlike RASMOL DEEP VIEW displays only in wireframe In addition a window called inputlog txt opens don t worry about this thus close it e Window pulldown Menu Go t
12. nter the molecule on one atom e Fit a molecule onto an other More advanced fitting features available in the Tools pulldown e Mutation tool e Torsion tool Allows to rotate sidechains atoms Page 8 of 11 Deep View Tutorial Introduction to Program Menu Pull downs e File Commands as most programs e Edit Commands as most programs e Select Provides commands for selection in addition to those in the Control Panel all selects all inverse selects opposite of what is selected visible selects those residues that are currently visible pick on screen selects those which you click on in the display group kind selects by amino acid nucleic acid heteroatom solvent or disulfide bonds group property selects based on acidity or polarity secondary structure selects alpha helices beta sheets or coiled accessible aa selects amino acids over a certain accessible cut off determined by user e Build Useful when rebuilding a model during a process called refinement For now don t worry about this menu e Tools Provides various advanced tools some of which we will discuss in later lessons e Fit Allows various operations such as superimposition of molecules This pulldown will only be active when more than one molecule is present e Display Allows options on different ways to display molecule The most important are o Show CA trace only o Show sidechains even when backbone hidden command noted in PAR
13. o the Window pulldown menu at the top of the Tool Bar window Scroll to the following to see its location and what each entails o Control Panel Opens to the right of the Display window The Control Panel is very important It lists the amino acids residues and other contents of the PDB file From here you select residues label residues color residues ect We will go into more depth in Part III of this tutorial thus do not close this window Page 3 of 11 Deep View Tutorial Introduction to Program O Alignment Opens below the Display window This window shows the amino acid sequence of the protein in one letter abbreviations This window comes in handy when comparing sequences of two or more proteins For now close this window Layers Infos Opens to the right above the Control Panel This table allows control of multiple protein models when needed You can choose which model is visible which model can move and which model has certain features displayed For now close this window Ramachandran Plot Opens to the left of the Control Panel As learned in lecture a Ramachandran plot allows you to judge the quality of a model and find residues whose conformational angles lie outside allowed ranges For now close this window PART II Moving your Model To make your model active click on the Display window The following Tool Bar buttons will manipulate your model Take time to play with these tools More to come on the Tool
14. unselected groups on the numeric key pad Toggles on and off the selected groups without affecting the other unselected groups Make sure you NUMBER LOCK IS ON Exercise Now Let s play with these a bit First scroll down to the bottom to see how many amino acids and the names of the hetero group s the protein contains Hetero group s are always listed last Select LEU 25 SER 36 Click and drag on the word LEU 25 through SER 36 These residues are now selected and should turn red Press Enter Notice only those residues selected residues 25 36 remain in the display window and have a check next to them in the show and side raws Move the display using the manipulation tools learned previously What type of secondary structure is this Note When using the Control Panel a sidechain is only shown if the residue is displayed You can display only the sidechains without the backbone by using the Show Sidechains even when Backbone is Hidden under the Display pulldown in the Tool Bar Click the checkmark in the show raw next to CYS 30 Notice that CYS 30 disappears Click in the same space to make it reappear Try the same in the Page 6 of 11 Deep View Tutorial Introduction to Program side label and surface raws and see what happens Now remove the checks from the label and surface raws simply by clicking on the checkmark e Click on the raw heading word label Notice all selected residu
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