[ Visualiser ]: Mapping a mesh to a pdb file

[Albert Solernou Crusat]

The blobs that we study represent proteins and often the structure of these proteins is known at the atomic level, stored in pdb files. It would be terrific if we could see the all atomic structure superimposed to the FFEA representation.

I can imagine different levels of complexity for this terrific feature that only exists in the wishlist: 1. The all atomic structure, is plot using some representation (sticks, ribbon or cartoon, see attached pictures) together with the mesh, though they only will fit correctly on the first snapshot. 2. The atomic structure is somehow flexible and we can see it on top of the mesh (or instead of the mesh representation) along the trajectory. 3. The atomic structure allows us to select certain atoms according of its type, chain, or molecule, and translate this selection into nodes, edges or faces. We could then either assign different colours/textures to this mesh items or save the selection into a file somehow (likewise in the "Edit VdW"). 4. Any combination of the previous features, and even showing scalar/vectorial values on top of the all atom structure.

In my opinion [1] and [3] would be more useful in scientific terms (although I can imagine that [3] may be pretty complex) than [2] and [4].

[xvysoc01]

Picture looks nice, but I need more information about pdb file format. Please send me a link to web page(s) about pdb.

[Albert Solernou Crusat]

Besides the pictures, there's already the correspoding .pdb file attached.

Popular visualisers are PyMOL: https://www.pymol.org/ (which can be installed through apt-get) and VMD: http://www.ks.uiuc.edu/Research/vmd/

You can find lots of pdb files in the Protein DataBase website: http://www.rcsb.org/pdb/home/home.do (though I don't think you'll need it)

[xvysoc01]

I made a VTK input file from .node file and than it is possible to plot VTK and PDB on one screen.

Problem is that both mesh and structure are on different position and with different rotation. I tried to set it during last hour, but the result is not much good. It is possible, however setting the same position is quite hard manual work.

Much easier is plot these objects in two different windows.

[Albert Solernou Crusat]

Mostly sorted out with the PyMOL plugin, one could think of combining it with Ben's Mesh->PDB mapper. We should add this to the repo/doc somehow.