Mini Map Aide: Difference between revisions

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[https://minimapai.de/ Mini Map Aide] is a mobile phone website application for visualizing atomic models and electron density maps. It emulates a small number of the functions of [[Molecular visualization in the 1980s|FRODO]]. It is coded in Lua, simply because that was the language that was stored in my head at the time of deciding to do this. Mini Map Aide uses a JavaScript virtual machine [http://fengari.io/ Fengari] so that it runs as a web-browser script and can use various javascript libraries such as [https://mathjs.org/ math.js] and, most importantly, the 3D graphics library [https://threejs.org/ three.js]. Quoting from [https://en.wikipedia.org/wiki/Three.js Wikipedia] (the free encyclopedia):  

Mini Map Aide attempts to mimic a tiny fraction of FRODO's protein rebuilding capabilities, albeit in a rather different way to be more amenable for use with mobile devices. On the dark display window there is a "Move" button which should always be active. When this is clicked or touched, the atoms in the residue which is currently at the centre of the display can be moved by small swipes on the screen. The moveable atoms are highlighted in a pale purple colour and a particular atom can be moved by touching it and gently swiping in one direction. The purple blob for this atom will swell for an instant to indicate that is has been selected. When the atoms have been moved to the desired locations, the geometry can be regularised and the bonds redrawn by clicking the "Tidy" button. The changes to the structure can then either be undone or saved as a new PDB file with the "Undo" and "Save" buttons, respectively.  

The option to tidy the geometry does so in a very simple stochastic way which is based on a table of approximate interatomic distances found in high resolution crystal structures of amino acids and polypeptides. These are all rounded to the nearest 0.1 &#8491;. The method calculates all of the deviations from the ideal distances within the rebuilt residue and the atom-pair with the worst distance deviation is targeted for correction. Consider two atoms that should be covalently bonded. Since we know the direction of the bond in 3D and how much the bond length needs to increased or decreased to correct it, we could move both atoms inwards or outwards along the bond vector by half the distance violation and get a perfect bond length, at the risk of worsening the geometry of other bonds which these atoms are involved in. Instead, the algorithm takes a slightly different approach which is to take one of the two atoms at random and move it by half of the calculated distance correction in the right direction and leave the other atom unmoved. At this point the deviations from ideal geometry for the whole residue are recalculated and the worst distance violation found and corrected in exactly the same way as before. The whole process is repeated until the worst distance violation is less than 0.1 &#8491;. The reason for choosing which of the two atoms to move completely at random is simply to stop the process becoming stuck trying to correct correlated distance violations cycle after cycle <i>ad infinitum</i>. It helps to prevent the algorithm getting stuck making the same two conflicting distance corrections over and over again.  

==Content Attribution==