This new sub-forum contains a set of algorithms to be used in conjunction with the MembraneEditor. [jar] files can be used with the standalone and the web start edition, [java] files can only be used with the standalone edition, but contain the source code. For more information on plugin development, please see:
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MembraneBoxifier [java]

Post by bjoern » 12.01.2015, 14:45


This small tool can be used to transfrom lipids to bounding boxes. For this purpose, the maximal distances of the different atoms are taken into account to create the 8 edges of a box.

With this algorithm, you can do two things:
  • Change the shapes of a previously generated membranes to boxes. This might not make much sense, but it is possible.
  • Generate boxified molecules, by first place a single molecule in a membrane model, then boxify it with this algorithm, then export it as a PDB file (rename it to, e.g., molecule_boxified.pdb) and then import this molecule.

3 important aspects:
  • If a membrane was already generated and you run the MembraneBoxifier, you have to refresh the geometry (Green Button saying: Refresh All 3D Objects in the Membrane).
  • If you want to generate the membrane by using boxified lipids, make sure that Shape Collision Detection is turned on in the 3D Settings Dialog! Otherwise, the collision will not work correctly because the algorithms will only take the extreme points into account.
  • Moreover, to get molecules as boxes, deactivate Automatic Detail Settings in the 3D Settings Dialog and move the three modifiers on the right side of the dialog to the minimum setting.
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developer: Björn Sommer

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