Hi Fernando,

Can't find any bad english in your email :-)

1: https://en.wikipedia.org/wiki/Marching_cubes

2: To open the isomesh again in PyMOL, I suggest to save a PyMOL session file 
(.pse). Getting access to the actual geometry is more tricky. There is a script 
on the PyMOLWiki which can convert isomesh and isosurface objects to CGOs. The 
script could be a starting point for you to export a custom file. The data is 
rather simple, just a sequence of vertices and normals.

3: VTK? scikit-image?


> On Feb 5, 2018, at 4:24 AM, Fernando Oliveira <fll.oliveira...@gmail.com> 
> wrote:
> Hi!
> This is my first e-mail to this list. Sorry in advance for my bad english.
> I've been using APBS for the past month in order to build protein binding 
> sites representations for a artificial neural network I've been working on. 
> At first I used the OpenDX output file from APBS stand-alone but I wanted to 
> generate Isomesh files aswell, in order to store the files conveniently for 
> future analysis or even to use as data input at some order work.
> 1- When APBS finished calculation, it creates a map object. But how does 
> PyMol translate the .dx map into that beautiful Isomesh? (achievable using 
> the Isomesh command aswell)
> 2- How to save that isomesh in a way I could open it again with Pymol or 
> another Visualization tool? (I already tried saving as .wrl. but I cannot 
> open it on Pymol and the file syntax is confusing)
> 3- Are there any other softwares or libraries to do such things? (output 
> isomesh at one specific level (5), store it in a convenient way, etc)
> Thanks for the attention.

Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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