UnityMol – SweetUnityMol User Manual
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1. GRAY 23 GLOW SweetUnityMol UserManual 24 SweetUnityMol UserManual FA mainly for sugar representation I don t have the surface representation for sugar This is because by default the surface representation for sugar molecule is disabled Like that you can easily represent a glycoprotein in surface mode and locate sugars molecule To be able to see the sugar surface click on Sugar toggle button present on the Surface Menu last element of this menu I have a sugar molecule but the SugarRibbons doesn t work It might be several causes for this issue 1 The 3 letters code for your sugar molecules in your PDB file is not recognize check Color code for monosaccharides page 13 a Change the 3 letters sugar name in your PDB by a recognized code b In Tune Menu uncheck Sugar Only And click on Enable SugarRibbons again maybe twice to uncheck then check again 2 You have a connectivity issues ring of 4 or 7 or more or 2 ring for 1 sugar a No solution here It s still a beta version and we have to fix that The RingBlending or SugarRibbons coloration is gray The 3 letters code for your sugar molecules in your PDB file is not recognize check Color code for monosaccharides page 13 How to make a screenshot without the Userlnterface Press backspace touch ese above Return touch Then press the P touch The screenshot is on the same folder of the PDB with the name testscreen x png with x the number of2. Texture Scale Hyperball Visualization Renderer Panels The Renderer and Panels menus are made to change the color and the texture of either the entire molecule or a selection Hide Radius 0 40 LOD mode Automove Atom selection 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 you are in Hyperballs mode and this option is checked when you will change the orientation of the camera the molecule will go back to the particle mode and then recreate the Hyperballs This is to be used 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 Hyperball Style A HyperBall Style menu 3 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 Interactive mode use spring forces to make an interactive molecule An atom c
3. a Glucose GLC Gulose GUL EST Idose IDO E Acide Ketodeoxynonulosonique KDN Acide Ketodeoxyoctulosonique KDO Manose MAN gt MMA 1 NAG i Acide neuraminique N glycolyl NEG L NDG NGA 1 Rhamnose RHA Ribose RIB NEN Acide Sialique SIA EE Tagatose TAG BE Talose TAL EI Xylose XYL 13 SweetUnityMol UserManual Examples Particles mode Smooth HyperBalls mode Default Smooth HyperBalls mode CPK Wan Der Waals Licorice Te 14 SweetUnityMol UserManual Texture CPK T an O lt x 15 Other examples Renderer Menu SweetUnityMol UserManual Coloration Mode Goodsell 16 SweetUnityMol UserManual cu y m 7 WaterColor o e D e 9 gt D Basic IUPAC 17 Chain Sugar DNA RNA SweetUnityMol UserManual 18 SweetUnityMol UserManual Secondary Structure Menu Secondary Structure N p A A gt 19 SweetUnityMol UserManual B factor NJ AN Surface Mode 20 SweetUnityMol UserManual Surface with static mobile Cut ES v V 7 ak d Ne pe 3 i D4 e po Ring Blending with sugar coloration SugarRibbons 21 Special Effect BLUR NOISE BLUR2 SweetUnityMol UserManual 22 SweetUnityMol UserManual DO a D EDGE n VORTEX
4. cut the surface and the cut will be the same when you change the camera s orientation Brightness adjust the brightness of the surface Color weight adjust the color concentration on the surface Electrostat To use this menu you have to have in the same folder as the PDB file and the same name a file dx and apf generate with softwares like APBS Software for evaluating the electrostatic properties of biomolecular systems Electrostatics Transparency T 0 Load Neg Load Pos Toggle Neg Toggle Pos Volumetric Fields Field Lines Transparency Add transparency to the mesh generated when you load 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 nene Screenshot or P key take a screenshot prefer the P key or you ScreenShot Sequence will get all menus with the capture BackGround Yes No ScreenShot Sequence doesn t work yet White Grey per Background add a picture in the background switch between yes no White Gray Black quick sele
5. the screenshot Be careful when you start a new session of SweeUnityMol the number x will start from O again So your previous screenshot will be remplaced a new version will fix that I fetch a PDB and when I use the ScreenShot function touch P I can t find my screenshot When you fetch a PDB the Screenshot function doesn t work the screenshot is saved in a folder who doesn t exist Will be fixed on a next version want to have a white background Display gt White I want to use the SugarColorationMode Atom Appareance gt Panels gt Sugar I want to use a Texture on Hyperballs Atom Appareance Renderer click on a sphere image you can apply your texture only on a selection with Residues Chain Extended atoms selection 25 SweetUnityMol UserManual I want to use a Texture on the Surface representation Surface gt Generate if you didn t do it again Surface gt Texture gt Click on a sphere image I want to represent a glycoprotein in SurfaceMode and the Sugar molecule in SugarRibbons Surface menu gt Generate Sugar Menu gt Enable SugarRibbons want to represent a glycoprotein in Hyperballs for amino acids and SugarRibbons for sugar You have to play with the Sugar Non Sugar checkbox in the Sugar Menu You may have to click twice on theses checkboxes issues with the Userlnterface Will be fixed on a next version For example with 3FUS from a new session of SweetUnityMol In the input PDB ID 3
6. FUS Fetch PDB Sugar gt Enable SugarRibbons Sugar Non Sugar twice Some bonds in my molecule is missing Our shader need OpenGl Use the file Run SweetUmol 32 bat or Run SweetUmol 32 bat depending your version the line has to be something like umol winXX 20141002 exe force opengl have a black screen or a part of the screen stay black Do not use the full screen mode check Windowed in the UnityMol Configuration menu this menu is the menu where you choose your resolution and click on Play We discover this issues with the news version of Unity3D We didn t locate where this problem is from 26
7. Navigation This 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 symmetry Symmetry direction vector of the symmetry direction Send activate the guided navigation mode Guided Navigation X Symmetry origin 34 3444 114 29016 69 0832 Symmetry direction 0 446105 0 001356 0 89494 Send This menu is made to deal with the specific features of sugar visualization principally made with the POLYS 2 0 software But the visualization mode Enable RingBlending called Ring Blending works with all molecules Enable SugarRibbons Enable Ring Blending enable the filling of all rings aromatic sugar or other cycle with a semi transparent color gt gt Hiding atoms 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 Sugar hide non sugar atoms Hide Hydrogens Sugar Non Sugar Tune Menu Tune Menu ee x Show Oxygens to display the intracyclic oxygen atom as a sphere Show Oxygens eee Sugar Only apply the sugar Ribbons vizualisation only on sugar residues will detect 3letters sugar code in the PDB file List of recognize ee 3 letters word bellow 1 00 Change Coloration open the Color Tune Menu to chang
8. UnityMol SweetUnityMol User Manual 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 unitymol sourceforge ne sweet Documentation input files and series of illustrations can be found at http glycopedia eu SweetUnityMol 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 Mav 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 4 JE v0 91 April 2013 Graphics Input Screen resolution 1360 x 768 IV Windowed Graphics quality Fantastic m Select monitor Display 1 left vl mr Our shader need OpenGl Use the file Run SweetUmol 32 bat or Run SweetUmol 32 bat depending your version the line has to be something like umol winXX 20141002 exe force opengl DO NOT USE THE FULL SCREEN MODE check Windowed in the UnityMol Configurati
9. an 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 x xe dp A SweetUnityMol UserManual B Rendered Menu 4 Atom Colors Textures and Scales Apply changes to Reset Extended atoms selection Residue All Chain All Color and Scale Panels Reset scales Scale 100 Texture Draw Style 1 Grayscale Panels Menu Color Panels All white Goodsell Watercolor Pastel CPK Basic IUPAC Chains ADMARMN Texture Panels Default GPK Acid Basic The whole molecule is selected by default The selection can be changed by e Atom Type A e Atomname B e Residue name C e By chain D You can combine your selection You have pre configured coloration on the Panels menu E and you can change the color of your selection by clicking on the Color Button F A texture can be applied to the selection G on your selection Several textures are available on other pages you can switch pages by clickiging lt lt and gt gt This menu contains pre configured colors You can switch b
10. ction of background color Background Color choose your background color with a color panel Effects add special effect Infos show hide FPS info and Atom Bond number Display Background Color Effects Infos List of all visual effects e SSAO Screen Space Ambient Occlusion Works on spheres cubes surfaces and secondary structures e BLUR add a blur effect when you move the camera e NOISE add noise on the screen e BLUR2 constant blur e DOF focus on a point and make fuzzy all atoms far from this point To use you have to be in Sphere mode Atoms gt Atom Style gt Sphere and click on an atom Works better for bigger molecules e CREASE doesn t work yet e EDGE the edge of every atom is black e VORTEX twist the molecule around the center e GRAYS make the molecule black and white e TWIRL similar to VORTEX e SEPIA use a SEPIA coloration e GLOW make all atoms shiny Advanced This menu offers advanced options some are being implemented GUI Scale change the size of the GUI Be aci ta a Ortho Persp doesn t work yet GUI Scale 0 76 Ortho Persp Best Textures don t use anymore Best Textures Off Depth Cueing Depth Cueing doesn t work yet Volumetric Depth Cueing Ambient Occlusion Volumectric Depth Cueing Doesn t work yet Ambient Occlusion darkens the densest parts of the molecule 8 SweetUnityMol UserManual to improve depth perception Guided
11. e Adjust the scale of the B factor used T Density threshold used to generate the isosurface Generate generate the surface BFactor adjust the shape of the surface according to the bfactor value Volumetric show the volumetric space of the protein with a particle system 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 Once you press the Generate button this window will appear Inside color Use atom color Use chain color Hydrophobic scale U rties color Use BFactor color Texture static cut Mobile cut Brightness 1 00 Color weight 0 50 SweetUnityMol UserManual 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 otf 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 Bfactor 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
12. e 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 C1 C4 bond for pyranose Pyranose to adjust the thickness of other bonds for pyranose Furanose to adust the thickness of bonds for Furanose Ribbons Thickness 0 15 Inner Ring Thickness 1 80 Outer Ring Thickness 1 00 Pyranose 6 C1 C4 Bond Thickness 0 20 Pyranose 6 Other Bond Thickness 0 16 Furanose 5 Bond Thickness 0 20 Reset parameters SweetUnityMol UserManual Color Tune Menu ColorTune Menu X For Oxygen Sphere Outer Rings and Bond OXYGEN SPHERE 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 open a color picker windows to choose a custom Custom color for Oxygen Outer Rings or Bonds You can make the color darker or lighter with the Light Color Factor slider Sugar Chain RINGS Sugar Chain Custom Color Lighter Color Factor Chain Custom Color Lighter Color Factor 0 35 VRPN This menu is used to connect a haptic arms but you need a VRPN server installed on your computer Work in progress MDDriver This menu is used to connect a molecu
13. lar simulation in real time Work in progress Reset 10 SweetUnityMol UserManual Binding Keys LEFT Arrow A 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 OD I ON CH 4 G2 PX I Cl Ga Co C4 C5 C6 FUC FUG FUG PUG BUE FUL BUE BUC FUC EUC BUC BUC FUC SweetUnityMol UserManual RA nn nan nn nan EE LO ss CUBO BS 0 e e Og k DO O 00 O OC D D D GC OO CO CO CO GO CO CO O Cl C2 e Ca OS C4 Ga Co 12 SweetUnityMol UserManual Color code for monosaccharides Monosaccharide Code Code Couleur A2G EN AAL 1 Abequose ABE EE Aceose ACE e Aldotetrose ALT Apicose API gt Arabinose ARA BGC m BMA EI Acide Dehydroascorbique DHA Fructose FRU mn Fucose FUC mm FUL a Galactose GAL GLB
14. on menu this menu is the menu where you choose your 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 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 October 2010 File PDB Loading Open File From Disk Proxy Server Proxy Port Please input a PDB ID 1K 42 Fetch PDB Read Hetero Atoms 1 Open a file from hard drive you can t change hard drive yet UnityMol and the pdb file have to be on the same drive but on different directories 2 Fetch a pdb from the pdb database if Proxy Server and Proxy Port are not empty please remove all fields otherwise the program will crash 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 Atom a ppearance by Atom or by Bond Atom Style Bond Style The preselected visualization called Hyperball the most interesting one HyperBall Hyperstick smooth HyperBalls Colar
15. y 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 SweetUnityMol UserManual e CPK CPK coloration with adapted texture secondary Structures Secondary structures Enable Secondary structures Helix Width 1 50 Sheet Width 1 70 Coil Width 0 30 Thickness 0 30 Helix diameter 1 80 Arrow width 1 80 Color by 55 Color by chain C alpha trace Bfactor Representation Surface Generate BFactor Volumetric HetAtoms Sugars Acid Basic coloration and texture according to the acid basic status of amino acids Secondary Structures Activate the Secondary Structure visualization Adjust parameters for the secondary structure visualization Color by secondary structure type Color by chain type Don t forget to click on this button to apply changes Trace the shape of the proteins by a spline passing by all carbon alpha Smoothness is used to adjust the smoothness of the trace Like the C alpha trace but adjust the radius and the color of each sphere with the B factor valu
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