MicroMégas User Manual
Contents
1. 3 is very tight around the atoms but almost the same as the default value of 2 7 0 01 gives a very coarse bigger and smoothed surface See Figure 4 The Group surface checkbox If you uncheck this checkbox then each chain will be meshed sepa rately into separate Graphite mesh objects Highlighting selected residues on the surface It is possible to select some residues and see their influence or localization on the molecular surface of the chain they belong to To do so enter a range of residues in the texfield to the left of the Select button Use the format r s r s N to indicate the selection of residues r rt 1 s You can enter several selections clicking on Select for each or using the syntax r1 S1 r2 S2 You will see that in the list the selections are numbered starting from 0 Color Before clicking on the Select button click on the colored rectangle to the right in order to choose the color of this group of residues You can change the default color for the non selected residues with the colorbox Base surface color In the main Graphite window you should see the new surface with its colors Moving a surface around It is possible to translate and rotate the mesh surfaces in Graphite by using surfaces a the surface tool ane MicroMegas ane MicroMegas gt NickoN gas O coe fliekoh gas oore PDB and Surfaces Distances Parameters PDB and Surfaces Distanc2. i tini i 1 N where t is the tangent vector and n is a normal vector to the curve at the sample point o The initial DNA strand One base pair is selected and twisted Note how all base pairs have been rotated accordingly Another pair is selected and twisted More pairs have been twisted Figure 6 Twisting DNA 6 2 Drawing the DNA strand For now we do not care about the precise nucleotides in the sequence so the sequence will be AAA We keep an atomic model of a base pair AT centered at the origin In order to draw the full DNA strand we instanciate the atomic 3D model at each sampling point o of Su in the frame f Moreover at frame fi we rotate the model by 2 to reproduce the DNA helix 6 3 A hierarchy for interactive visualization and base pair picking We build a binary hierarchy over the sequence of frames f i 1 N The root node consists of the entire sequence The subsequence at one node is split in two sub subsequences to form the two child nodes At each node a sphere bounding all the sampling point in the subsequence of the node is computed When drawing a long DNA strand the hierarchy is traversed top down and if the bounding sphere of the node is sufficiently far away alternative simpler drawing of the sub sequence are used Our implementation uses a double ribbon model for intermediate distances and a simple line for faraway strands The hier
3. point on C that form a linear approximation of the curve such that the angle between two consecutive segments is below some threshold The adaptive sampling is used to display a visually smooth curve while minimizing the number of segments used in the linear approximation of the curve We also use an uniform sampling S of P in which consecutive samples point on the curve are equally spaced along the curve We using a spacing close to 3 4 to obtain a unifom sampling S in which the sample points will serve as the anchor point for base pairs of DNA 6 1 A rigidly moving frame From the above we have obtained a uniform sampling S of the curve together with the tangent vector at every sample point In order to coherently orient the base pairs in space along the curve we need to augment this data with a normal vector so as to obtain an orthonormal frame at each sample point Many simple methods to do so result in a sequence of frames exhibiting discontinuities or strong torsion eg the Frenet frame But ideally we would like the sequence of frames to be as rigid as possible without discontinuities and minimizing torsion in order to be a good start for orienting the DNA base pairs This is not an easy ask but the work Wang et al shows how one can obtain an extremely good approximation at a very low computational cost WJZLO08 After computing a normal vector at each sample point of S in this way we store the sequence of triple f o
4. MicroM gas User Manual Samuel Hornus September 26 2011 Abstract The MicroM gas plugin for Graphite adds the possibility to 1 manipulate curves e edit quadratic and cubic B zier curves e load interpolatory curves a sequence of points e display these curves in various styles including as a DNA strand e edit the precise orientation of the base pairs around the curve e export the obtained DNA strand in the PDB file format 2 generate protein surfaces e display the model chain hierarchy of PDB files e mesh various part of a protein with various meshing options e specify intervals of residues and colorize these intervals e export the surfaces in a 3D file format e compute inter residue distances 1 Setting up MicroM gas To enable the MicroM gas plugin follow these steps 1 2 Open the Graphite s preferences window File preferences Click on the Modules tab Make sure that the MicroMegas appears in the list If not type MicroMegas in the textfield on the right of the Add button and click on this button then click on the Save configuration file button and restart Graphite Click on the GEL tab Check that a file named micromegas gel appears in the list If not add it by clicking on the small folder icon below selecting the correct file in lib plugins OGF MicroMegas and clicking the Add button then click on the Save configuration file
5. again this will only recompute the colors not the surface except if you change the blending see below or if you force a remesh for example after you change the Precision parameter After a while look at the Info at the bottom of the MicroM gas window a triangular mesh of the surface appears in the main Graphite window The name of the generated surface depends on the selected item and looks like mm_pdb name model name chain name but you can change it afterwards Figure 2 Left The two chains in 2cfa pdb are meshed without blending one has some blue color the other has some yellow color The two meshes intersect Right After checking the Blend chains checkbox the two chains are blended together The ReMesh checkbox Ifa mesh with that name already exists see paragraph above then the surface is not re computed only the colors are recomputed If you really want to recompute the mesh you should either rename delete the already existing mesh or check the ReMesh checkbox The Blend chains checkbox If you check the Blend chains checkbox and more than one chain are going to be meshed when you select a PDB or a model then the chains will be blended as if it was only one chain This can be useful if you intend to keep these chains together with a beautiful triangular mesh Figure 2 The Precision textfield lets you enter a value between 0 01 and 3 than controls the coarseness of the molecular surface
6. archy and its bounding sphere is also used to efficiently compute which base pair has been clicked on by the user when he wants to manipulates the DNA see below 6 4 Twisting the DNA strand Since our goal is the modeling of DNA strand in interaction with some proteins it is important that the user user be able to fine tune the position of the DNA atoms at least locally when there is a strong interaction with the outside world Allowing independent atom placement while most powerful would destroy the curve model that we use to make DNA modeling easier Instead we allow the adjustment of the rotation of each base pair around the curve That is at each frame f the base pair is rotated by angle Zin a i Where a is specified by the user More precisely a 0 initially and the user can then modify the angle of each base pair individually To avoid the tedious task of setting the value of a for all 2 the values are interpolated where they are not specifically defined Suppose that the user has defined the values a a a with i1 lt ig lt lt ug Then the value of a is computed as follows ifi lt i1 then a ai e if i gt ik then a Qi aij ij 1 z i T Qigay i ij if tj lt 1 lt iei then ay 3 4 4 j 1 J Figure 6 illustrates DNA twisting References DFH09 Nira Dyn Michael S Floater and Kai Hormann Four point curve subdivision based on iterated chordal and centripeta
7. button and restart Graphite If setup correctly a separate MicroM gas window should open when you start Graphite Figure 1 You can close this window at any time and reopen it from Graphite s menu Window Show MicroMegas window The bottom textfield The horizontal text field at the bottom of the MicroM gas window simply displays information about what is going on 2 Molecular surfaces The length unit in MicroM gas is the Angstrom A We use the molecular surface model of A Fast Method of Molecular Shape Comparison A Simple Application of a Gaussian Description of Molecular Shape J A Grant M A Gallardo and B T Pickup Journal of Computational Chemistry Vol 17 No 14 1653 1666 1996 For generating molecular surfaces we use the PDB eng MicroMegas and Surfaces tab of the MicroM gas window Fig Nickes Close ure 1 PDB and Surfaces Distances Parameters Load PDB Delete PDB Opening a PDB selecting models and chains Mocs ee Click on the button Load PDB for opening a PDB file The loaded PDB files appear in the first column named PDB If you click on a PDB file name oo the list of models it contains appears in the middle Select Reject column named Models When you click on a model ORE number the list of chains it contains appears in the Precision 2 7 NIRE right column named Chains Blend chains Group surfaces Y Selected residues Mesh Surface an
8. d Colorize Info Which chains are going te be meshed At any given time there is exactly one PDB selected or there is exactly one model selected or there is exactly one chain selected This is important as this is the way to select which set of chain s is going to be meshed Figure 1 The main window of the MicroM gas plu gin e if a PDB is selected then all its chains are going to be meshed into one Graphite s mesh object one surface possibly with several connected components see below e if a model is selected then only the chains belonging to that model are going to be meshed into one mesh object e if a chain is selected then only that chain will be meshed into one mesh object Which residues are defined When you select a chain by clicking on it in the Chains list a text ap pears to the right just above the Selected residues caption This texts starts with Defined residues and is followed by a list of integers intervals Each number in these intervals corresponds to a residue whose atoms are present in the PDB file If a number is not in one interval then you cannot select the correspond ing residue for color highlighting see below because there is no residue corresponding to this number in the PDB file Creating a surface Use the Mesh Surface and Colorize button to compute a mesh of the chains If you change the selected residues in some chain for showing them in special colors click the button
9. es Parameters Residue 1 Residue 2 Distances Mesher s distance bound in Angstrom 0 15 Chain 1 Chain 2 Res Res Add pair Recompute distances Remove selected pair Info Info Figure 3 The Distances tab left and the Parameters tab right of the MicroM gas window Tip I find the following settings best for visualizing molecular surface disable the lighting in the shader parameters and enable the Ambient Occlusion via Window Fullscreen effect 3 Inter residues distances In order to compute inter residues distances we use the Distances tab Figure 3 The left part of that tab lets the user select pairs of residues among the loaded PDB with a self explanatory interface Whe the pair is chosen a click on the Add pair button will add the chosen pair of residues to the list of pairs on the right Two buttons below let the user Recompute the distances or Remove the pair that is selected in the list of pairs While it is possible to translate and rotate the mesh surfaces in Graphite in particular those generated by meshing a protein s surface the affine transformation is not yet applied back to the atoms positions and thus the distances will not change Applying the transformation to the atoms is part of the future work 4 Parameters tab In this tab Figure 3 you can set the following The Mesher s distance bound roughly controls the maximum distance between the mesh appr
10. is displayed in the info text field at the bottom of the graphite s window e Clicking outside of the DNA unselects the selected base pair e Holding down the right mouse button and moving the mouse horizontally modifies the orientation of the selected base pair around the curve That orientation can be modified in the range 7 7 e A middle click removes the rotation constraint on the selected base pair When using the Atoms display option of the Curve shader the base pairs with a rotation constraint are visually lighter than the other pairs in order to make it easy for the user to see which pairs have rotation constraints From the constrained base pairs a precise orientation is computed for all every base pair so as to keep the DNA as naturally twisted as possible For example when exactly one base pair has a rotation constraint that constraint is propagated to all base pairs when the user modifies this constraint the whole DNA strand can be seen to rotate around its central curve Figure 6 illustrates DNA twisting 6 Technical details on DNA modeling We choose to use a smooth curve C to model DNA at any point on the curve the tangent vector must be well defined So must be the arc length from the start of the curve to that point Currently in MicroM gas two type of curves can be edited quadratic and cubic B zier curves Two point samplings of C are used an adaptive sampling Sa of C consists of a sequence of
11. l parameterizations Computer Aided Geometric Design 26 3 279 286 2009 WJZLO8 Wenping Wang Bert J ttler Dayue Zheng and Yang Liu Computation of rotation minimizing frames ACM Transactions on Graphics 27 1 2 1 18 March 2008
12. mera is sufficiently close to the curve A DNA lines mode makes the shader displays two ribbons in place of the DNA strand One motivation for these tools is to let the user coil a virtual DNA strand around proteins Further the rotation of indivual base pair around the curve s axis can be set as desired Then the DNA strand can be exported in the PDB file format The curves can be saved to disk and reloaded but currently the tuning of base pairs around the curve s axis are not saved 5 1 Editing curves A new curve is created by using the Scene gt create object command and choosing the Line type The curve is then edited with the tools depicted in Figure 5 Two tools blue green are for quadratic B zier curves two pink for cubic B zier curve These tool let the user e add control points at the end of the curve e delete split and move any control point See the on screen mini manual for the details of the tools 5 2 Editing DNA base pairs Before tuning the base pairs orientation around the curve the user must set the Curve display option to Atoms or DNA_lines ribbons once so as to generate a uniform sampling of the curve necessary for the tool to work properly e A left click is used to select a base pair which the user wants to manipulate For technical reason clicking closer to the central curve works better The selected base pair is indicated visually with a yellow ring around it and its number along the curve
13. oximation of a molecular surface and the real molecular surface A higher number results in simpler meshes A smaller number results in dense but ultra smooth meshes Default value is 0 15A See Figure 4 A Sal ision Prec 0 5 g O H n H Prec 0d i1sion Prec Distance bound OK X S vaN DIAZ AAN 0 05 ays Ka X s SLE TP uN Z AK 3 ALNA AZT 0 15 0 5 Various meshes of 2VAW pdb Figure 4 Figure 5 Inside the red rectangle the tools that the MicroM gas plugin adds to Graphite NOTE a fifth button for manipulating individual base pairs of the DNA strand is not yet depicted on this early screenshot 5 Curve editing for DNA The MicroM gas plugin adds various methods to edit 3D curves It also provides facilities to construct a as rigid as possible moving frame at fixed arc length intervals along the curve Quadratic and Cubic B zier curve are support for creation and editing Figure 5 A high quality interpolatory scheme DFH09 is available as well for dealing with input data in the form of a point list No editing facilities is provided for interpolatory curves we set this as low priority future work MicroM gas provides a shader for such curves whose name is Curve A particular interest of this shader is that it uses the aforementionned rigidly moving frame to enable the drawing of pseudo DNA strand with level of details LOD showing the atoms when the ca
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