UnityMol – SweetUnityMol User Manual (Version Nov
Contents
1. sta y D e Y da L E N 4 ZA SugarRibbons 21 Special Effect BLUR NOISE BLUR2 SweetUnityMol UserManual 22 SweetUnityMol UserManual I EDGE ss u U Ba VORTEX GRAY 23 GLOW SweetUnityMol UserManual 242. A2G HE AAL Abequose ABE Aceose ACE Aldotetrose ALT DL Apicose API Lo Arabinose ARA BGC i BMA TT Acide Dehydroascorbique DHA Fructose FRU Fucose FUC ER FUL a Galactose GAL GLB Glucose GLC Gulose GUL Idose IDO Acide Ketodeoxynonulosonique KDN Acide Ketodeoxyoctulosonique KDO Manose MAN I MMA 3 NAG mr Acide neuraminique N glycolyl NEG I NDG NGA DL Rhamnose RHA Ribose RIB NEN Acide Sialique SIA EE Tagatose TAG BE Talose TAL E Xylose XYL 13 SweetUnityMol UserManual Examples Particles mode Smooth HyperBalls mode Default Smooth HyperBalls mode xp x Wan Der Waals Licorice Be gt Texture CPK Acid Basic SweetUnityMol UserManual 15 Other examples Renderer Menu SweetUnityMol UserManual Coloration Mode Goodsell 16 SweetUnityMol UserManual cu gt re tu 9 WaterColor g gt Basic IUPAC 17 Chain Sugar DNA RNA SweetUnityMol UserManual 18 SweetUnityMol UserManual Secondary Structure Menu Secondary Structure p 4 A gt 19 B factor SweetUnityMol UserManual Surface Mode 20 SweetUnityMol UserManual Surface with static mobile Cut UN De be NA YN e M s IS 2 T4 he DE w ms Ring Blending with sugar coloration
3. E check Windowed in the UnityMol Configuration menu this menu is the menu where you the resolution and click on Play Description of the coordinate input file see Annex Ring Color Coding see Annex SweetUnityMol UserManual Main Menu File Atoms Sec Structures Surface Electrost Display Advanced Guided Nav Sugar VRPN MDDriver Reset Some of these options offering advanced visualization and manipulations haptic arm are being implemented and are not functional at this time November 2014 1 Open a file from hard drive you can t change hard drive yet UnityMol and the pdb file have to be Open File From Disk on the same drive but can be located on different directories File PDB Loading Proxy Server Froxy Port Please input a PDB ID 2 Fetch a pdb from the pdb database TT Fetch PDB if Proxy Server and Proxy Port are filled please remove all fields otherwise the program will crash Read Hetero Atoms By default the visualization of UnityMol is the Particle mode This mode uses the particle system of Unity3D to display the molecule This may not be the most appropriate visualization Changing to SmoothHyperballs mode offers a better visualization Atom Different types of representations are available Ata ADODEHAIAHNICE un td ss by Atom or by Bond Atom Style Bond Style The preselected visualization is called Hyperball the most interest
4. UnityMol SweetUnityMol User Manual Version Nov 2014 Installing the software The software described below has been developed based on revision 676 of UnityMol and version4 5 2f1 of Unity3D All source code was implemented using C and Cg languages built into Unity 3D and is available along with executables for Mac Windows and Linux platforms on the sourceforge project website http sourceforge net projects unitymol files Documentation input files and series of illustrations can be found at http glycopedia eu IMG pdf unitymol user manual pdf Windows version date 2014 10 02 32 bits umol win32 20141002 Data Run SweetUmol 32 bat umol win32 20141002 exe 64 bits umol win64 20141002 Data Run SweetUmol 64 bat umol win64 20141002 exe Mac version date 2014 10 02 umol macosx universal 20141002 app Linux version data 2014 10 02 umol linux 20141002 Data umol linux 20141002 x86 umol linux 20141002 x86 64 SweetUnityMol UserManual Running Windows version 32 and 64 bits UnityMol Configuration q v JE v0 91 April 2013 Graphics Input Screen resolution 1360 x 768 IV Windowed Graphics quality Fantastic Select monitor Display 1 Left ce Gen The shader needs OpenGl Use the file Run SweetUmol 32 bat or Run SweetUmol 64 bat depending upon your version the line has to look like umol winXX 20141002 exe force opengl DO NOT USE THE FULL SCREEN MOD
5. d the cut will remain the same upon changing the orientation of the camera Brightness adjust the brightness of the surface Color weight adjust the color concentration on the surface Electrostat To use this menu the following files have to be in the same folder the PDB file and the same name a file dx and apf generated with softwares such as APBS Software for evaluating the electrostatic properties of biomolecular systems Transparency IM Load Neg Load Pos Toggle Neg Toggle Pos Volumetric Fields Field Lines Transparency Add transparency to the mesh generated upon loading the negative and positive electrostatic visualization T Threshold used to generate the electrostatic isosurface Load Neg Pos load electrostatic visualization Toggle Neg Pos show or hide the electrostatic visualization Volumetric Fields volume rendering of the electrostatic fields Field Lines show the Field Lines visualization examine the local intensity of electric fields SweetUnityMol UserManual Display This menu is made to take screenshot change the background and add special effects STE Screenshot or P key take a screenshot prefer the P key or you will get all menus with the capture Dis play BackGround Yes No ScreenShot Sequence doesn t work yet White Grey Black Background add a picture in the background switch between yes no White Gray Black quick selection of bac
6. e mode use spring forces to make an interactive molecule An atom can be dragged and he will go back to his original position Drag Spring spring parameters for interactive mode Velocity Colors colors each atoms in interactive mode with the velocity of each one Interactive mode Measure dist Measure dist activate and click on 2 atoms to dispaly their distance Dist cueing Dist Cueing adjust the light according to the distance of the camera Exemple Ball amp Sticks Licorice VdW Smooth Hyperballs EEE SweetUnityMol UserManual B Rendered Menu 4 Atom Colors Texture Scale Atom Colors Textures and Scales The whole molecule is selected by default Apply changes to Reset The selection can be changed by None e Atom Type A e Atomname B Extended atoms selection e Residue name C Residue All e Bychain D Color and Scale Panels The selection can be combined Texture Draw Style 1 Pre configured coloration is on the Panels menu E Another color can be by clicking on the Color Button F A texture can be selected and applied to the selection G Several textures are available on other pages you can switch pages by clickiging lt lt and gt gt Panels Menu Color Panels All white Goodsell Watercolor Pastel CPK asic IUPAC Chains ADNARN Texture Panels Default CPK Acid Basic This menu contains pre configured colors You can sw
7. his menu is used to make a guided navigation but for now it works only with the pdb 3EIO GLIC as part of work in progress Symmetry origin X Y Z coordinates of the center of suided Navigation Symmetry origin Symmetry direction Enable RingBlending Enable SugarRibbons Hide Hydrogens gt gt Hiding atoms Sugar Mon Sugar Tune Menu Tune Menu show Oxygens Sugar Only Oxygen Sphere Size 1 00 Ribbons Thickness 0 15 Inner Ring Thickness 1 80 Outer Ring Thickness 1 00 Pyranose 6 C1 C4 Bond Thickness 0 20 Other Bond Thickness Pyranose 6 0 16 Furanose 5 Bond Thickness 0 20 Reset parameters 34 3444 0 446105 symmetry Symmetry direction direction Send activate the guided navigation mode 4 29016 vector of the symmetry This menu is made to deal with the specific features of sugar visualization the atomic coordinate file can be generated pdb format by several molecular builders but the POLYS 2 0 software is the most appropriate The visualization mode called Ring Blending works with all molecules Enable Ring Blending enable the filling of all rings aromatic sugar or other rings with a semi transparent color Enable SugarRibbons enable the SugarRibbons visualization to transform a sugar into a schematic representation like secondary structures but adapted for sugars Hide Hydrogens hide hydrogens atoms Sugar hide sugar atoms Non Suga
8. ing HyperBall Hyperstick one smooth HyperBalls Color Texture Scale Hyperball Visualization Renderer Panels Hide The Renderer and Panels menus are made to change the color and the texture of either the entire molecule or a Atom selection selection Radius 0 40 LOD mode Automove Lock camera Brightness 1 00 Hide Hide the molecule This option is activated when some visualization SweetUnityMol UserManual option like secondary structures is activated Uncheck this box to display both the secondary structure and the molecule Radius Change the radius of spheres LOD mode when in the Hyperballs mode and this option is checked and upon changing the orientation of the camera the molecule will be displayed in the particle mode prior recreating the Hyperball representation This is to be used for large macromolecular systems for which the Hyperballs representation reduces frame rate too much FPS Frame Per Second Automove or SPACE key the camera will turn around the molecule Lock Camera The camera will not be able to move when this option is checked Brigtness Adjust the brightness of Hyperballs i A HyperBall Style menu 3 Hyperball Style Shrink 0 50 Shrink To adjust the shape of the bond Scale 1 00 Scale To adjust the scale of the bond DFactor only for Biological Networks Metaphor Metaphor pre configured style CPK Licorice VdW Smooth Hyperballs Interactiv
9. itch by clicking on the buttons Color Panels e All white make the molecule all white e Goodsell make the color softer e WaterColor color carbons in blue e Pastel default colors e CPK color with the CPK color code e Basic color carbon in green e IUPAC color with the IUPAC color code e Chains color by chain e Sugar color by sugar Type the molecule must contain sugar e ADN ARN coloration for DNA and RNA Texture Panels e Default default texture e CPK CPK coloration with adapted texture SweetUnityMol UserManual e Acid Basic coloration and texture according to the acid basic status of amino acids Secondary Structures Secondary Structures SE Activate the Secondary Structure visualization Enable Secondary structures Helix Width 1 50 Sheet Width 1 70 en Adjust parameters for the secondary structure visualization Thickness 0 30 Helix diameter 1 80 Arrow width 1 80 inst Color by secondary structure type Color by chain type Color by 85 Color by chain Don t forget to click on this button to apply changes Trace the shape of the proteins by a spline passing by all alpha carbons Smoothness is used to adjust the visual aspect of the trace C alpha trace Bfactor Representation Like the C alpha trace but adjust the radius and the color of each sphere to the B factor value Adjust the scale of the B factor used Surface T Density threshold used
10. kground color Background Color choose your background color with a color panel Effects add special effect Infos show hide FPS info and Atom Bond number Background Color Effects Infos List of all visual effects SSAO Screen Space Ambient Occlusion Works on spheres cubes surfaces and secondary structures BLUR add a blur effect upon moving the camera NOISE add noise on the screen BLUR2 constant blur DOF focus on a point and make fuzzy all atoms away from this point This has to be used while being in the Sphere mode Atoms gt Atom Style gt Sphere and requires selecting by clicking an atom Works better for large molecules CREASE doesn t work yet EDGE the edge of every atom is black VORTEX twist the molecule around the center GRAYS make the molecule black and white TWIRL similar to VORTEX SEPIA use a SEPIA coloration GLOW make all atoms shiny Advanced This menu offers advanced options only some are implemented 4 GUI Scale change the size of the GUI Sn Ortho Persp doesn t work yet GUI Scale 0 76 Ortho Persp Best Textures don t use anymore Best Textures Off Depth Cueing Volumetric Depth Cueing Ambient Occlusion Depth Cueing doesn t work yet Volumectric Depth Cueing Doesn t work yet Ambient Occlusion darkens the densest parts of the molecule to improve depth perception SweetUnityMol UserManual Guided Navigation T
11. open a color picker windows to choose a custom color for Oxygen Outer Rings or Bonds The color can be made darker or lighter with the Light Color Factor slider This menu is used to connect a haptic arm but a VRPN server needs to be installed on the computer Work in progress 10 SweetUnityMol UserManual Binding Keys LEFT Arrow Move LEFT RIGHT Arrow D Move RIGHT DOWN arrow S Move DOWN UP arrow W Move UP Q Rotation DOWN E Rotation UP X Rotation LEFT N Rotation Right B ZOOM P ZOOM P Screenshot only on local pdb BACKSPACE Hide GUI SPACE Automove R Reset to center C Center to one or several atoms select an atom with the selection mode Guided Navigation only for 3EIO U Constrained Navigation UP panoramic mode J Constrained Navigation DOWN panoramic mode panoramic mode Numpad or B Spreading chains Numpad or V Narrowing chains Numpad or T Reset chains Format of the PDB File ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM oo lt ON GE NE CL C2 ibis C4 CD C6 BUC BUE FUG PUG BUE FUL BUE BUC FUC EUC BUG BUC FUC SweetUnityMol UserManual PRPPRPRPRPRPRPHEHRRPHPE EE LO A a 0 U Bo NI NX e e OT E GN DO O 00 9 EOL D D D OO CO GC 00000090 Cl C2 e C2 se C4 Ga Co 12 SweetUnityMol UserManual Color code for monosaccharides Monosaccharide Code Code Couleur
12. r hide non sugar atoms Tune Menu Show Oxygens to display the intracyclic oxygen atom as a sphere Sugar Only apply the sugar Ribbons vizualisation only on sugar residues will detect the 3 letter sugar codes in the PDB file List of recognized 3 letters code is given below Change Coloration open the Color Tune Menu to change color of sphere rings and outer ring Oxygen Sphere size To adjust the size of the radius of the sphere Ribbons Thickness to adjust the thickness of the ribbon Inner Ring Thickness to adjust the thickness of the ring Outer Ring Thickness to adjust the thickness of the ring Pyranose to adjust the thickness of the glycosidic bond for pyranose Pyranose to adjust the thickness of other bonds for pyranose Furanose to adjust the thickness of bonds for Furanose VA B F IVa 4 L p YO RE i AE Er T a m mm gt MI o CIICK ON AL FR u Dr gt sq s Re PRE E Color Tune Menu ColorTune Menu OXYGEN SPHERE Sugar Chain Custom Chain Custom Color Lighter Color Factor Chain Custom Color Lighter Color Factor VRPN Reset MDDriver This menu is meant to visualize a real time molecular simulation Work in progress SweetUnityMol User Manual For Oxygen Sphere Outer Rings and Bond Sugar use the sugar color to color Oxygen Outer Rings or Bonds Chain use the chain color to color Oxygen Outer Rings or Bonds Custom color
13. to generate the iso surface Generate generate the surface BFactor adjust the shape of the surface according to the B factor value BEacior Volumetric show the volumetric space of the protein with a particle system Volumetric Toggle surface hide surface representation when you change a parameter you have to hide the surface and press the Generate button again HetAtoms Sugars show surface for HetAtoms or and Sugars molecules HetAtoms SweetUnityMol UserManual Upon selecting the Generate button this window will appear Inside color Use atom color Use chain color Hydrophobic scale Use properties color Use BFactor color lexture Static cut Mobile cut Brightness 1 00 Color weight 0 50 Color change the color of the surface external face Inside color change the inside color Use atom color Color the surface according to the type of atom under each portion of it Use chain color use the color of the chains Hydrophobic scale Color the surface according to different hydrophobic scale of residues Use properties color Color the surface according to the properties of amino acids basic acids etc Use BFactor color Color the surface according to the B factor value of the surface atoms Texture apply a texture on the surface Static cut cut the surface you can control the cutting by a pad that will appear in the upper right corner Mobile cut cut the surface an
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