If you want to save atoms, bonds and surfaces and load them into Chimera later, then save a session, menu File / Save Session As…. Tom

On Jul 31, 2018, at 3:38 AM, ⁨עמיחי הולצר⁩ <⁨amiholz@gmail.com⁩> wrote:

When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)? I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh?

Thanks, Amichai

2018-07-30 19:37 GMT+03:00 Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>>: Hi Amichai,

Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command

https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>

Tom

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On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩ <⁨amiholz@gmail.com <mailto:amiholz@gmail.com>⁩> wrote:

Hi Chimera support,

I have 2 questions:

1. How does Chimera calculate the mesh from the density map?

2. How can I save the mesh as a file?

Thanks a lot, Amichai Holzer Huji _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>