Re: [PyMOL] On APBS, Isomesh generation and export

[Thomas H. <tho...@sc...>]

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.
https://pymolwiki.org/index.php/Dump2CGO

3: VTK? scikit-image?

Cheers,
  Thomas

> On Feb 5, 2018, at 4:24 AM, Fernando Oliveira <fll...@gm...> 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.