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.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. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
