How to generate 3D Mesh from APBS map? (like Pymol Visualizations)
Entering edit mode
3.7 years ago

Hi! First post here.

I've been working on creating a deep learning model to evaluate the docking protocols (pose binding prediction) I'm performing on peptide fragments and I've been planning on using electrostatics surface (using focused calculation through APBS suite) as binding site representation, as already implemented in other works. Other than that, I would like to have a way to visualize my data. In Pymol, after the calculation of the Map is finished, the results can be displayed as a 3D Isomesh of the grid calculated by APBS.

What I want is to save this Mesh produced as another file.

I already tried saving it as wrl but the formating is not that good for my purposes (i.e. I cannot extract the information of a given point[x,y,z] and calculate basic statistics on several points).

1- Is there any other file format to save such meshes on PyMol? (already read much of the Wiki and mailing list)

2- Are there any other softwares, scripts, magical tomes to create such maps from the .dx (OpenDX format) output from APBS?

Thank you

pymol machine learning isomesh • 1.1k views
Entering edit mode
14 months ago

have the same question. I would like to evaluate the electrostatic potential in certain points at the mesh. Do you come with any answer?

Best Regards.


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